Small RNA Annotation


Non-coding or small RNAs (miRNA, lincRNA, snoRNA, snRNA, tRNA) can be annotated by aligning to genomic sequence or predicted by comparison to sequences in a databases e.g. miRBase. Small RNA analysis can include:

  1. end trimming
  2. alignment against erroneous sequence (mtDNA, primers, adapter dimers, rRNAetc.)
  3. alignment of filtered reads against the full genome and other databases
  4. classification of short reads into known small RNA categories
  5. absolute and relative read counts
  6. discovery of novel miRNAs (depending on read depth)
  7. identification of differentially expressed miRNAs based on read tags

Providers offering Small RNA Annotation (found 15)


Omega Bioservices

NGS provider United States of America

Our facility is unique because we offer the full range of NGS service from sample extraction through to data analysis. Sample extraction capabilities and expertise cover the entire spectrum of both environmental and clinical sample types.

Years in service: 7

Other services offered by Omega Bioservices:

Service Description Price
Differential Gene Expression Analysis Identify differentially expressed genes among samples using RNA-seq technique. Human, mouse, rat, fruit fly, cattle, pig, chicken, zebrafish, C. elegans, maize, thale cress, Japonica rice (Oryza sativa) and yeast, up to 7.5gb/sample. $56.00 USD (per sample)
Differential Gene Expression Analysis Custom bioinformatics for non-model organisms, or other unusual cases. Does not include setup fee. $110.00 USD (per sample)
Transcriptome Mapping Map mRNAs to either the reference or the assembled genome. $332.00 USD (per sample)
Custom scripting and special projects We are open to your custom analysis projects. Set up a call with our Project Scientist team today to discuss your needs and obtain a quote. $500.00 USD (per sample)
Read Filtering and Cleaning Examination of sequencing quality and removal of low quality reads prior to downstream analysis provided free of charge with sequencing service if desired. $110.00 USD (per sample)
Exome Analysis Whole exome sequencing involves capturing the coding region of the genome, or exons (EXpressed regiONS). SNVs and indels are the most important and abundant types of variation in exons. Human exome analysis provided free of charge with sequencing service. $332.00 USD (per sample)
ChIP-Seq Analysis ChIP-Seq is a technique to identify DNA loci bound by a specific protein. The standard output of ChIP-seq analysis includes peak call and motif enrichment at binidng sites. $332.00 USD (per sample)
Small RNA Mapping Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. $221.00 USD (per sample)
SNP / Indel Mapping Mapped to the reference genome and annotated using public database. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
Genome Mapping Genome mapping is a technique used to assign the location of a particular gene on a chromosome and measure their relative locations and distances between genes. Mapping to many model organisms provided free of charge with sequencing service. $110.00 USD (per sample)
Metagenomic Analysis Metagenomic analysis involves the identification and quantification of genetic material from environmental, uncultured microorganisms. Analysis involving only 16S rRNA amplicon sequences are provided free of charge with sequencing service. $551.00 USD (per sample)
SNP / Indel Calling Identify SNPs and Indels in the region of interested, using DNA sequencing. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
SNP/SV/CNV Discovery Variants discovery. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
Targeted Capture Analysis Variant call, gene annotation. Provided free of charge with sequencing service. $332.00 USD (per sample)
Genome Annotation Annotation is the process by which pertinent information about these raw DNA sequences is added to the genome databases. This involves describing different regions of the sequence and identifying which regions can be called genes. $221.00 USD (per sample)
Small RNA Annotation Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. $332.00 USD (per sample)
Methylation Analysis The processing of bisulfite sequencing data includes sequence alignment and the quantification of absolute DNA methylation at base resolution. Methylation analysis for data generated from the Illumina TruSeq kit are provided free of charge with sequencing service. $553.00 USD (per sample)
Transcriptome de novo Assembly Identify and quantify putative mRNA transcripts using RNA-seq data for unannotated species. $553.00 USD (per sample)
Transcriptome Annotation Annotate or predict functions of transcribed genes using well know gene ontology tools. $332.00 USD (per sample)
Variant Annotation Identified variants will be mapped to the reference genome and annotated using public database. Analysis for human sequences provided free of charge with sequencing service. $332.00 USD (per sample)
Whole Genome de novo Assembly Prices vary according to genome type. Please contact our Science Project Team. Some small genome assembly provided free of charge with sequencing service. $3315.00 USD (per sample)
Base Calling Demultiplex data and convert BCL files to FASTQ files $110.00 USD (per sample)

Parseq Lab

Czechia

Parseq Lab is experienced in: - massively parallel sequencing data analysis - client-tailored algorithms and software development - analysis pipelines deployment

We offer: - whole genome/exome and targeted sequencing data analysis - de novo assembly - SGV detection and annotation - expression analyses - metagenomics analysis - transcriptomics analysis - proteomics research - genuine task-specific workflows design - custom bioinformatics applications development - statistical data analysis

Collaborations: genomic research labs, sequencing facilities, academic and research institutions.

Years in service: 8

Other services offered by Parseq Lab:

Service Description Price

Next Generation Intelligence

NGS provider Italy

NGI is a platform for Next Generation Sequencing data analysis. We offer a wide range of bioinformatics tools and an experienced and professional collaboration service for any type of biological data analysis. We provide both standard and customized analysis, custom softwares and pipelines development and post-sequencing support. We'll enhance and make easier your discovery process.

Expertise:

Our expertise is in the epigenetics field in mouse and human organisms.

Infrastructure:

we will provide FTP access to our storage server to upload raw data and download analyzed data.

Other services offered by Next Generation Intelligence:

Service Description Price
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
Base Calling Inquire
Targeted Capture Analysis Inquire
Differential Gene Expression Analysis Inquire
Genome Mapping Inquire
Small RNA Mapping Inquire
Exome Analysis Inquire
Transcriptome Mapping Inquire
Genome Annotation Inquire
Transcriptome Annotation Inquire
Custom scripting and special projects Inquire
Transcriptome de novo Assembly Inquire
Other Services Inquire
SNP / Indel Mapping Inquire
Small RNA Annotation Inquire
SNP/SV/CNV Discovery Inquire
Methylation Analysis Inquire
ChIP-Seq Analysis Inquire
Variant Annotation Inquire

ecSeq Bioinformatics

Germany

Bioinformatics solutions

ecSeq provides a variety of bioinformatics service packages suited for most everyday high-throughput sequencing experiments. We are particularly engaged in RNA-seq projects (trancriptomics, differential expression), ncRNA analysis (small RNA-seq, ncRNA annotation) and epigenome sequencing (bilsufilte and methylation analyses). Further bioinformatics solutions include SNP calling, variant annotation & prioritisation as well as development of customized algorithms.

Public workshops and eTrainings

We develop eTrainings and provide workshops for employee training in bioinformatics. Several times a year, we organize well-attended workshops on selected topics in next-generation sequencing data analysis. Test datasets are used for getting started in applying and developing bioinformatic tools.

Topics covered by our workshops include:

  • RNA-seq bioinformatics
  • Sequencing technolgies
  • Small RNA-seq data analysis
  • Genomic data visualization
  • Perl for bioinformatics
  • Programming in R

Expertise:

We have long experience in the development and application of bioinformatics methods to high-throughput sequencing experiments. These methods have been successfully applied in various experimental designs ranging from ncRNA and mRNA sequencing to genome/epigeome analyses. We have worked with sequencing data from humans, lifestock species (chicken, cow, turkey), plants and bacteria. Our employees are continuously involved in projects from national and international consortia, like the International Cancer Genome Consortium (ICGC) or the Leipzig Research Centre for Civilization Diseases (LIFE).

Infrastructure:

We have access to moderate computation resources allowing us to process ~120GB sequence data per week.

Other services offered by ecSeq Bioinformatics:

Service Description Price
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
ChIP-Seq Analysis Inquire
Genome Mapping Inquire
Variant Annotation Inquire
Small RNA Mapping Inquire
Transcriptome Mapping Inquire
Small RNA Annotation Inquire
Methylation Analysis Inquire
Custom scripting and special projects Inquire
SNP / Indel Mapping Inquire
Transcriptome Annotation Inquire
Differential Gene Expression Analysis Inquire
Exome Analysis Inquire
SNP/SV/CNV Discovery Inquire

Bioinformatics Unit, Panacea Biosciences

NGS provider India

Other services offered by Bioinformatics Unit, Panacea Biosciences:

Service Description Price
Custom scripting and special projects Based on project requirements. $15.00 USD (per hour)
Read Filtering and Cleaning $40.00 USD (per sample)
Exome Analysis End to End Exome-Seq Data Analysis $75.00 USD (per sample)
ChIP-Seq Analysis we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. $80.00 USD (per sample)
Genome Mapping Available only for Human, Mouse and available sequenced geneomes $75.00 USD (per sample)
SNP/SV/CNV Discovery End to End variant analysis $70.00 USD (per sample)
Small RNA Annotation Available only for Human, Mouse and available sequenced geneomes $60.00 USD (per sample)
Base Calling Base calling is the process of assigning bases (nucleobases) to chromatogram peaks. One computer program for accomplishing this job is Phred base-calling, which is a widely used basecalling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy. $50.00 USD (per sample)

ContigExpress, LLC

United States of America

ContigExpress is the leading integrated genomics data service provider. We offer genomic project management, data analysis, and bio-IT consulting services. Our unique value to our clients lies in our deep understanding of both biology and informatics. From project consultation, bio-IT infrastructure implementation, to data analysis, our experienced scientists deliver not only cost-effective customized informatic solutions but also their expert insights.

Our team consists of Ph.D.-level computational biologists with extensive training and professional practice in bioinformatics and genomic research. We understand both your cutting-edge research and your informatics challenges. We enable you and your team to extract actionable information from the vast amount of genomic data in a cost-effective and timely fashion.

We at ContigExpress strive to deliver affordable expert genomic data solutions to researchers and clinicians. We place the utmost emphasis on information confidentiality, data security, and data integrity. Please schedule a complimentary project discussion with one of our expert bioinformaticians to discover how we can help you move your genomics research forward!

Years in service: 10

Other services offered by ContigExpress, LLC:

Service Description Price
ChIP-Seq Analysis Following is a list of common analysis items for ChIP-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Peaking calling with or without control samples 5) Gene assignment and peak annotation ... Inquire
Differential Gene Expression Analysis Following is a list of common analysis items for RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Gene and transcript-based quantitation, RPKM/FPKM-based quantitation, Raw hit count-base... Inquire
Genome Annotation Following is a list of common analysis items for Genome Annotation. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Gene prediction with or without RNASeq data 3) BLAST-based gene function annotation 4) Written project report with analysis methods, publication-ready gra... Inquire
Genome Mapping Following is a list of common analysis items for Whole Genome Resequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP/small indel ch... Inquire
Methylation Analysis Following is a list of common analysis items for Methylation Sequencing, including MeDIP-Seq, hMeDIP-Seq, RRBS / Targeted Bisulfite-Seq, WGBS, and 5-mc RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Methylation state-sensitive mapping 4... Inquire
Transcriptome Annotation Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Project consultation 2) Transcriptome annotation (molecular functions, Gene Ontology and pathway) 3) Written project report with analysis methods, publication-ready graphics, and references Inquire
Exome Analysis Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) S... Inquire
Metagenomic Analysis Following is a list of common analysis items for Metagenomics Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Sequence assembly 4) Biodiversity analysis and binning 5) Gene predication and functional annotation 6) Gene Ontology and pa... Inquire
Small RNA Annotation Following is a list of common analysis items for small RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC, adaptor removal, and size selection 3) Read characterization by mapping to a reference genome sequence, known RNA families (e.g., Rfam), and known mi... Inquire
Small RNA Mapping Following is a list of common analysis items for small RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC, adaptor removal, and size selection 3) Read characterization by mapping to a reference genome sequence, known RNA families (e.g., Rfam), and known mi... Inquire
Targeted Capture Analysis Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) S... Inquire
Transcriptome de novo Assembly Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Transcriptome assembly, scaffolding and gap closure 4) Gene annotation (molecular function, Gene Ontology and pathways) 5) SNP di... Inquire
Whole Genome de novo Assembly Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Contig assembly 4) Scaffolding and gap closure 5) Gene/ORF prediction 6) Gene annotation and classification via database search a... Inquire
Other Services We are a professional bioinformatics service provider and we are happy to provide customized informatic solutions to your unique research and business needs. Please feel free to reach out to us to discuss how we can help you. Inquire
SNP/SV/CNV Discovery Following is a list of common analysis items for Whole Genome Resequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP/small indel ch... Inquire

Station X

United States of America

We offer a powerful genomics software platform that makes various bioinformatics tasks fairly straightforward to perform and deliver to customers. We also wrap this product with various service offerings for folks interested in one-off projects that deliver results rather than just subscribing to a software solution and then do the work themselves. We are comfortable with both scenarios. We are well versed in working with RNA-Seq, Genomes, Exomes, targeted panels, miRNA-Seq, Copy Number, Gene Expression, Protein Expression, and DNA Methylation from the level of raw sequencing reads or chip data all the way through to statistically-driven and knowledge-driven interpretations.

Expertise:

We are experienced in developing bioinformatics pipelines, providing data management solutions, analyzing the data using statistical methods and knowledge driven methods, and delivering professional-grade results. We are most familiar with human genomics projects, but have experience with other organisms as well. We are most focused on supporting sequencing projects, but are very capable of supporting array and PCR-based projects as well.

Infrastructure:

We leverage Amazon Web Services for most of our storage (EBS & S3) and computational resources (EC2). We are not frivolous about security, and we can provide you with security documentation to demonstrate how we leverage cloud resources while keeping best-in-class security. We also have powerful 16-core machines in our own private cloud that we leverage for service projects as well.

Years in service: 9

Other services offered by Station X:

Service Description Price
Exome Analysis $2500.00 USD (flat price)
Differential Gene Expression Analysis $1655.00 USD (flat price)
Small RNA Annotation $85.00 USD (per sample)
Small RNA Mapping $100.00 USD (per sample)
SNP / Indel Calling $100.00 USD (per sample)
SNP / Indel Mapping $100.00 USD (per sample)
Transcriptome Annotation $85.00 USD (per sample)
Variant Annotation $85.00 USD (per sample)
Custom scripting and special projects $275.00 USD (per hour)
Comparative Genome Analysis $2500.00 USD (flat price)
SNP/SV/CNV Discovery $100.00 USD (per sample)
Read Filtering and Cleaning $115.00 USD (per sample)
Other Services Visualizations, Report Generation, Customizations to our platform, Training, Scientific support, Presentation support, etc. $300.00 USD (per hour)
Genome Annotation $85.00 USD (per sample)
Transcriptome Mapping $100.00 USD (per sample)

Leucine Rich Bio

India

Other services offered by Leucine Rich Bio:

Service Description Price
Read Filtering and Cleaning Leucine Rich Bio offers Read filtering, cleaning and quality control analysis. We also offer statistical and heuristic analysis. Literature mining services are also provided. As we are Bangalore (India) based company, we offer very competitive pricing. $75.00 USD (per sample)
Transcriptome Annotation Inquire
Small RNA Annotation Inquire
Transcriptome Mapping Inquire
Comparative Genome Analysis Inquire
Variant Annotation Inquire
Differential Gene Expression Analysis Inquire
Targeted Capture Analysis Inquire
SNP / Indel Calling Inquire
SNP / Indel Mapping Inquire
Transcriptome de novo Assembly Inquire
Exome Analysis Inquire
Whole Genome de novo Assembly Inquire
SNP/SV/CNV Discovery Inquire
Custom scripting and special projects Inquire
Genome Annotation Inquire
Genome Mapping Inquire
ChIP-Seq Analysis Inquire
Metagenomic Analysis Inquire
Microbiome Analysis Inquire

Beckman Coulter Genomics

NGS provider United States of America

Beckman Coulter Genomics offers next generation sequencing services designed to meet the evolving sequencing needs of academic, biotechnology and pharmaceutical researchers worldwide. A comprehensive range of next generation sequencing services is available utilizing platforms from Illumina and Roche.

End to end solutions are offered allowing tailoring of projects to your specific needs. A wide variety of bioinformatics packages are available and results consultation is provided to ensure you understand the data returned to you. For the quickest service we accept pre-made libraries for sequencing only projects.

• Expert scientists consult on project design to ensure appropriate experimental approach • Beckman Coulter instrumentation utilized for fully automated library construction and target enrichment with enhanced reproducibility and reliability • Bioinformatics scientists oversee all data analysis to ensure quality
• Videoconference provided for report review and results discussion

Trusted Partner • Over 20 years sequencing experience • 1,500+ customer publications • 200+ successful audits • Experienced staff from well-known institutes of academic and commercial excellence • Contributed sequencing data to • >10 genome projects including mouse, cat, dog and salmon • >100 Microbial and Fungal genomes

Years in service: 14

Other services offered by Beckman Coulter Genomics:

Service Description Price
Read Filtering and Cleaning Inquire
Differential Gene Expression Analysis $150.00 USD (per sample)
Small RNA Annotation $150.00 USD (per sample)
Targeted Capture Analysis $250.00 USD (per sample)
Variant Annotation $250.00 USD (per sample)
Exome Analysis $250.00 USD (per sample)
SNP / Indel Calling $250.00 USD (per sample)
Metagenomic Analysis Assembly including demultiplexing and standard run report Inquire

NXT-Dx

NGS provider Belgium

At NXT-Dx we can offer SE50, PE50 and PE100 sequencing on the Illumina HiSeq. On top of this we can also offer different sequencing settings on the Illumina MiSeq and shortly we will also be able to offer sequencing on the Illumina NextSeq.

We can offer sequencing of already prepared libraries but we can also offer full-scope projects whereby we receive cells, tissue, gDNA or RNA and take care of the sample preparation, library prep, sequencing and bio-informatics analysis.

We have worked with samples from all kind of species (mammalian, plant, bacterial) and all kind of cell types.

We pride ourselves in having close contact with our customers and only one single contact point. Also after the delivery of the data, we remain available to answer any questions customers might have on their data, their analysis, etc.

Years in service: 8

Other services offered by NXT-Dx:

Service Description Price
Differential Gene Expression Analysis $170.00 USD (per hour)
Transcriptome Mapping $170.00 USD (per hour)
Comparative Genome Analysis $170.00 USD (per hour)
Custom scripting and special projects $170.00 USD (per hour)
Read Filtering and Cleaning $170.00 USD (per hour)
Exome Analysis $170.00 USD (per hour)
ChIP-Seq Analysis $170.00 USD (per hour)
Small RNA Mapping $170.00 USD (per hour)
Genome Mapping $170.00 USD (per hour)
Targeted Capture Analysis $170.00 USD (per hour)
Genome Annotation $170.00 USD (per hour)
Small RNA Annotation $170.00 USD (per hour)
Methylation Analysis $170.00 USD (per hour)
Transcriptome Annotation $170.00 USD (per hour)
Variant Annotation $170.00 USD (per hour)
Base Calling $170.00 USD (per hour)

SciBerg

Germany

We offer computational analyses of Next-Generation Sequencing data (Illumina and Ion Torrent platforms), including RNA-seq, small RNA-seq, DNA-seq, Bisulfite-seq and ChIP-seq. Our bioinformatics support can be fully customized for your research needs, the scope and objectives of the study. We apply only up-to-data well-proven software and pipelines working under Unix/Linux environment. Optionally, our experts can help to interpret the obtained results from the scientific point of view, provided some of them are working in a close research field.

Other services offered by SciBerg:

Service Description Price
Differential Gene Expression Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Transcriptome Mapping Inquire
Custom scripting and special projects Inquire
Other Services Inquire
Exome Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
ChIP-Seq Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
SNP/SV/CNV Discovery Inquire
Genome Annotation Inquire
Small RNA Annotation Inquire
Methylation Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire

DREAMgenics

NGS provider Spain

We offer bioinformatics analysis services for human and other organisms genomic and transcriptomic NGS data.

  • Our team of experts offers a completely personalized consulting service, including scientific and technical solutions to your needs. We help you to obtain the best results from your analysis.

  • Our collaboration with the most reliable sequencing providers allow us to select the most suitable platform for your project. We also can assist you in all steps prior to sequencing, such us sample and library preparation and quality controls.

  • DREAMgenics bioinformatics framework has been designed to readily adapt to your needs. Capable of integrating your own algorithms, pipelines and databases to complement the data analysis and interpretation.

  • Our analyses identify high quality genomic variants through excellent sensitivity and specificity standards, extracting meaningful biological information and reducing validation process costs. The results will be delivered through a detailed report.

  • We offer the possibility of advanced visualization and interactive review of results through our exclusive DG Reports web application. (Filtering and priorization of variants, Pre-classification of variants, Graphic interface (genomic browser), Statistics and quality controls, Exportable information, Automated generation of reports).

All our procedures meet with the requirements set by the new General Data Protection Regulation.

Years in service: 8

Other services offered by DREAMgenics:

Service Description Price
ChIP-Seq Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Exome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Base Calling https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Comparative Genome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Custom scripting and special projects https://www.dreamgenics.com/en/bioinformatics-services/ https://www.dreamgenics.com/en/research-projects/ Inquire
Other Services - Research projects https://www.dreamgenics.com/en/research-projects/ - Bioinformatics software design and developments https://www.dreamgenics.com/en/hd-genome-one-en/ - Gene and/or regions of interest panels, ATAC Seq, Family studies, trio analysis.. https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Differential Gene Expression Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Genome Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Genome Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Metagenomic Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Methylation Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Microbiome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Read Filtering and Cleaning https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP / Indel Calling https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP / Indel Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP/SV/CNV Discovery https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Targeted Capture Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome de novo Assembly https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Variant Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Whole Genome de novo Assembly https://www.dreamgenics.com/en/bioinformatics-services/ Inquire

ideas4biology Ltd.

Poland

DATA ANALYSIS Routine NGS data analysis in the area of genomics and transcriptomics, such as: - Gene expression and differential expression analysis - De novo and ab initio transcriptome assembly - Small RNA analysis - Genome variant calling and annotation

Customized tasks, including: - Identification of long noncoding RNAs - Identification of ta-siRNAs - Isomir and miRNA editing analysis - Annotation of non-model organisms - Building transcriptome-wide maps of RNA-RNA interactions

WORKSHOPS We offer workshops in a broad spectrum of bioinformatics applications, including: - RNA-Seq data analysis (4 days) - NGS in medical research (4 days)

EXPERIENCE We’ve been in the market since 2013 and came into collaboration with hundreds of customers. We’ve been working on model and non-model organisms, including viruses, bacteria, fungi, plants, animals, and human. We are part of research consortium aiming at development of personalized medicine services for diagnosis and treatment of lung cancers. We are also actively conducting research projects in different areas of genomics and transcriptomics, which gives us expertise in standard and up-to-date bioinformatics solutions.

INFRASTRUCTURE We have access to dedicated file storage and computational servers, with virtually unlimited (on demand) capacity.

Years in service: 6

Other services offered by ideas4biology Ltd.:

Service Description Price
Differential Gene Expression Analysis This includes: - quality filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - read mapping - expression estimation - differential expression analysis - a report, result data files and diagnostic plots Differential expression analysis itself, with expression estimations from customer: $30. $185.00 USD (per sample)
Transcriptome Mapping This includes: - quality check and filtering - adapter trimming - optional: discarding rRNA-mapping reads and other contaminants - read mapping (default or customized settings) - read mapping report and result files $100.00 USD (per sample)
Other Services Identification of long noncoding RNAs in animals and plants. This includes: - assessment of protein-coding potential with at least two independent methods - sequence length filtering - discarding of known, coding transcripts - discarding known noncoding RNAs other than lncRNAs - optionally: genomic context-driven filters - other filtering steps, depending on data availability, such as tr... $50.00 USD (per hour)
Read Filtering and Cleaning This includes: - Quality report - Quality filtering - Adapter trimming - Optionally: discarding rRNA-mapping reads or other contaminants $46.00 USD (per sample)
Small RNA Mapping This includes: - quality check and filtering - adapter trimming - read mapping to custom sequences (genome, transcriptome) - read mapping quality assessment - read mapping report This may be followed by miRNA identification or similar tasks, priced separately. $130.00 USD (per sample)
Genome Mapping This includes: - quality check and filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - read mapping with varied tools and settings - accomodated to customer's needs - quality report $85.00 USD (per sample)
SNP / Indel Calling This includes: - quality check and filtering - adapter trimming - read mapping and further processing of mapping results - SNP / Indel calling Both somatic and germline variants may be called. There is possibility to call structural variants as well, priced separately. $165.00 USD (per sample)
Small RNA Annotation This includes: - quality check and filtering - adapter trimming - read mapping to databases of noncoding RNAs, such as miRBase, DASHR or RFAM - annotation report $150.00 USD (per sample)
Methylation Analysis This includes: - quality check and filtering - adapter trimming - read mapping - calling methylated and unmethylated cytosines - differential methylation analysis: finding differentially methylated bases and regions $250.00 USD (per sample)
Transcriptome de novo Assembly This includes: - quality check and filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - transcriptome de novo assembly - a quality report and a transcriptome in FASTA format For further annotation of the transcriptome, please see our offer for "Transcriptome annotation". $250.00 USD (per sample)
Transcriptome Annotation This includes: - BLAST searches against databases of proteins and noncoding RNAs, including miRBase, RFAM, UniProt (Swiss-Prot) - hmmscan search against PFAM protein domains - assignment of GO terms to genes - assignment of KEGG pathways to genes - a report and annotation files with per gene details $125.00 USD (per sample)
Variant Annotation This includes: - prediction of possible consequences associated with predicted variants, such as affecting splicing of protein coding capacity - comparison with known variants from public databases - a report and result files $150.00 USD (per sample)

RealSeq Biosciences Inc.

NGS provider United States of America

Somagenics has an exceptionally fast turnaround time as fast as one week. We are especially experienced in library construction from small RNAs. Small RNA libraries are prepared using SomaGenics’ proprietary RealSeq® technology, the leader in bias reduction for small RNAs as shown by a core-facility comparison (ABRF). The starting input requirement for total RNA is as low as 1ng (RealSeq®-AC technology) or may be isolated from as little as 50ul of biofluid samples (RealSeq®-biofluids technology). We are experienced working with plasma, serum, whole blood and serum samples. Somagenics delivers fast and cost-effective mRNA sequencing services using either Nugen or NEB sequencing library preparation.

Years in service: 1

Other services offered by RealSeq Biosciences Inc.:

Service Description Price
Differential Gene Expression Analysis Reads processing and alignment. For each sequenced library: - Trimming of adapters - Alignment to the correspondent genome - We will provide raw files and processed (fastq and SAM files) mRNAs quantification - Align reads to reference transcriptome - We will provide mRNA reads counts (raw reads) Differential expression analysis (up to six groups) - Must have more than one sample 'per group' -... $50.00 USD (per sample)
Differential Gene Expression Analysis Reads processing and alignment. For each sequenced library: - Trimming of adapters - Alignment to the correspondent genome - We will provide raw files and processed (fastq and SAM files) mRNAs quantification - Align reads to reference transcriptome - We will provide mRNA reads counts (raw reads) Differential expression analysis (up to six groups) - Must have more than one sample 'per group' -... Inquire
Other Services Reads processing and alignment. For each sequenced library: - Trimming of adapters - Alignment to the correspondent genome - We will provide raw files and processed (fastq and SAM files) miRNAs quantification - Align reads to miRBase - We will provide miRNA reads counts (raw reads) Differential expression analysis (up to six groups) - Must have more than one sample 'per group' - Spreadsheet in... $50.00 USD (per sample)
Other Services Reads processing and alignment. For each sequenced library: - Trimming of adapters - Alignment to the correspondent genome - We will provide raw files and processed (fastq and SAM files) miRNAs quantification - Align reads to miRBase - We will provide miRNA reads counts (raw reads) Differential expression analysis (up to six groups) - Must have more than one sample 'per group' - Spreadsheet in... Inquire
Small RNA Annotation For organisms with a reference genome; or closely related species, we can run your FASTQ data through the miRdeep2 pipeline and give you the output files and a report that helps guide you in the organization of these files. Note, this is a freely available program and must be cited if used: (https://github.com/rajewsky-lab/mirdeep2) Cite: Marc R. Friedländer, Sebastian D. Mackowiak, Na Li, Wei ... $975.00 USD (flat price)

Genevia Technologies

Finland

Genevia Technologies provides a wide range of microarray and next generation sequencing data analyses, and bioinformatics services to life science companies and academia. In addition, we offer bioinformatics consulting projects at a fixed price, and genome-wide experiments done in collaboration with the top service providers.

Expertise:

Our expertise is in handling multiple microarray (expression, copy number, ChIP, methylation, etc) and next-gen sequencing (DNA-seq, RNA-seq, MeDIP-seq, ChIP-seq, GRO-seq, etc) data simultaneously and effectively, and combining them with other data such as clinical variables or pathway information. We have experience in most common mammalian systems, but especially in multiple human cancers. We have also worked on data from multiple species of lower eucaryotes and bacteria.

Infrastructure:

We have access to dedicated file storage servers, a computing cluster, a computing grid (of over 1000 CPUs), and cloud computing capabilities.

Visit our homepage to read more about us and our bioinformatics as a service: www.genevia.fi

Other services offered by Genevia Technologies:

Service Description Price
Methylation Analysis Inquire
SNP / Indel Calling Inquire
Base Calling Inquire
ChIP-Seq Analysis Inquire
Targeted Capture Analysis Inquire
Variant Annotation Inquire
Small RNA Mapping Inquire
Comparative Genome Analysis Inquire
Small RNA Annotation Inquire
Transcriptome Annotation Inquire
Custom scripting and special projects Inquire
SNP/SV/CNV Discovery Inquire
Other Services Inquire
SNP / Indel Mapping Inquire
Read Filtering and Cleaning Inquire
Differential Gene Expression Analysis Inquire
Transcriptome Mapping Inquire
Metagenomic Analysis Inquire
Transcriptome de novo Assembly Inquire