Essentials tools for working with high-throughput sequencing data:
bowtie -- bowtie-bio.sourceforge.net/
my current NGS aligner of choice
samtools -- samtools.sourceforge.net/
essential. the lingua franca for working with the output of alignment
picard -- picard.sourceforge.net/
also essential for working with alignment files. very nicely complements samtools.
fastx toolkit -- hannonlab.cshl.edu/fastx_toolkit/
this looks like it will be handy... though not yet part of any of the ubuntu software repositories I regularly use, it does look like it is included in the upcoming Oneiric Ocelot 11.10 upgrade.
cutadapt -- code.google.com/p/cutadapt/
may be made obsolete by fastx toolkit
Other useful resources, not necessarily singularly focused on sequencing data:
Bioinformatics manual at UC Riverside -- manuals.bioinformatics.ucr.edu/
Includes lots of good stuff on R and HTS data analysis
Statistical Computing pages at UCLA -- www.ats.ucla.edu/stat/
Provides very useful examples for different stats packages, very well organized.
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