Links to other Next Gen Sequencing resources

When adding a link, if possible add a line or two about what it's about, what you like about it, etc.

• http://seqanswers.com/ - “Your source for next gen sequencing information”. Has an active Bioinformatics forum at http://seqanswers.com/forums/forumdisplay.php?f=18 and one of their most useful and linked to topics is Software packages for next gen sequence analysis

• http://groups.google.com/group/solexa - general solexa talk - including wet lab protocols
• http://groups.google.com/group/sge-lifescience-sig/ - useful discussions on the solexa pipeline and how it can be run on Sun Grid Engine

• http://www.genographia.org/portal/topics (started by Clive Brown and co at the Sanger). Excellent resource for solexa quality/ troubleshooting, pipelines etc.
• http://www.sanger.ac.uk/Users/lh3/seq-nt.html Heng Li's list of nextgen software.

• http://nebc.nox.ac.uk/tools/bioinformatics-docs/high-throughput-seq - NEBC Next Generating Sequencing Information and Links page

FOSS = Free and open source software

• MAQ - Mapping and Alignment with Quality. Pros - great visualization tool, lots of options for information extraction.
• SOAP - Short Oligonucleotide Alignment Program - adv over MAQ = speed, ability to detect 1-3bp indels, trimming of 3' end where low quality bases are more likely.

For managing, analysing next gen sequencing data

• Roche 454 Genome Sequencer
• FinchLab
• CLCBio Genomics Workbench
• NextGene
• WikiLIMS