We wil be updating this page frequently with useful sequencing-related resources for researchers. If you have any suggestions for additional resources please use the feedback box at the bottom of the page to let us know.

Designing Sequencing Studies

• Genohub Sequencing Guide

Guide for determining read depth, coverage and other essential information for those new to Next Generation Sequencing.

• Genohub NGS Library Preparation Kit Guide

  Description of all library preparation kits and techniques offered on Genohub.

• Comparison of Next-Generation Sequencing Systems

Useful review describing the differences between HiSeq, Roche 454 GS FLX, SOLID and Sanger 3730xl.

• Field Guide to Next-Generation DNA Sequencers

Excellent guide that compares sequencing platforms, describing their strengths and weaknesses for various NGS applications.

Online Calculators

Coverage

• Genohub's sequencing matching system

This calculator not only determines the amount of coverage needed for a particular Next Generation Sequencing run, but also displays the service providers who offer sequencing services based on your results.

• Coverage calculator

Calculates the number of Illumina HiSeq or MiSeq sequencing lanes needed based on your required coverage.

Oligonucleotide

• Oligonucleotide Properties Calculator

Allows you to calculate Tm, chance that your oligo will self dimerize or form a hairpin structure. Also has Blast and mfold feature.

• IDT's OligoAnalyzer 3.1

Allows you to calculate Tm, chance that your oligo will self dimerize or form a hairpin structure. Also has Blast and mfold feature, along with the ability to use modified bases in your calculations.

Primers

• NCBI Primer-BLAST:

Find primers specific to your PCR template.

• Primer3: WWW primer tool

Allows you to pick primers from any DNA sequence.

qPCR Efficiency

• qPCR efficiency calculator

This calculator gives the amplification efficiency of a qPCR reaction based on the slope of the standard curve.

• QPCR Standard Curve Slope to Efficiency Calculator

Calculator to convert the slope produced by a qPCR standard curve to % efficiency.

Sequencing-related Industry News Sites

• GenomeWeb
• GenEng News
• Bio-IT World

Sequencing-related Blogs

• Genohub Blog
• RNA-Seq Blog
• CoreGenomics
• Pathogens Genes and Genomes
• BitesizeBio
• Omics! Omics!
• Genomes Unzipped
• In Between Lines of Code
• Kevin’s GATTACA World
• Next Generation Technologist
• Blog @ Illumina
• Personalized Genes

Sequencing-related Forums

• SEQanswers
  Popular online forum for the sequencing and bioinformatics community

• BioStars
  Bioiformatics Q&A Site

Open-Source Bioinformatics Tools

• SEQanswers Software Wiki
  A tabular view of a large number of open-source and commercial software tools

• NCBI Tools
  A small collection of NCBI tools such as the Amino Acid Explorer and BLAST

• Lab7 BioBuilds
  Lab7's BioBuilds package is a collection of pre-built binaries for common bioinformatics tools. BioBuilds is available for most Linux variants and OS X. Tools in BioBuilds run "out-of-the-box", with all dependencies included. Lab7 offers next generation sequencing pipeline and workflow management software and services.

• Galaxy
  Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

• The Genome Analysis Toolkit
  Software package developed at the Broad Institute to analyse next-generation resequencing data. It's free for academic use. Parts of the package are closed-source for commercial use.

• BioPython
  A set of freely available tools for biological computation written in Python by an international team of developers

• BioPerl
  A toolkit of perl modules useful in building bioinformatics solutions in Perl

Educational Material

• Genomics and Computational Biology
  MIT course taught by Dr. George Church available via OpenCourseWare

• UC San Diego Bioinformatics Algorithms on Coursera
  Free course covering algorithms underlying some fundamental topics in bioinformatics

• A Biology Primer for Computer Scientists (PDF)
  A short ground-up biology primer by Franco P. Preparata (Brown University)

• Molecular Biology for Computer Scientists (PDF)
  Free chapter from the book 'Artificial Intelligence and Molecular Biology' by Lawrence Hunter

• Computational Biology: Genomes, Networks, Evolution
  A more recent version of the computational biology course offered by the EECS department at MIT. Includes detailed lecture notes and has a focus on algorithms.