Software

Users can access software in /jgi/tools.  The available tools are listed below for your reference. 

In the future NERSC will create software modules and details regarding software maintenance and access will be found here.

programming languages
perl 5.10.1
R 2.14
python 2.6 and 2.7
ruby 1.9.2 and 1.8.7
java 1.6 and 1.7

other software and tools
abyss http://www.bcgsc.ca/platform/bioinfo/software/abyss
picard
bowtie
igv (Integrated Genomics Viewer from Broad)
gassst
http://bioinformatics.oxfordjournals.org/content/early/2010/08/24/bioinformatics.btq485
samtools
tabix
GATK
Mosaik
bwa
blast+
blastall
vcftools
filo https://github.com/arq5x/filo
velvet http://www.ebi.ac.uk/~zerbino/velvet/
stampy
mercurial http://mercurial.selenic.com/
uclust
usearch
MUMmer
FastTree
emboss
clustalx
clustalo
amos
TopHat
CuffLinks
decypher (Timelogic binaries)
ESTmapper http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page
MetaCluster
Celera  http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-7.0/
jellyfish
Broad's AllPaths http://www.broadinstitute.org/science/programs/genome-biology/crd
Broad's Arachne mira assembler
quake
echo
sga
newbler
megan
fasttree  http://microbesonline.org/fasttree/
smashcell  http://asiago.stanford.edu/SmashCell
tablet  http://bioinf.scri.ac.uk/tablet/index.shtml
hmmer 3.0  http://hmmer.janelia.org/
concavity  http://compbio.cs.princeton.edu/concavity/
sqlite  http://www.sqlite.org/
TagDust  http://bioinformatics.oxfordjournals.org/content/25/21/2839.full
muscle  http://www.drive5.com/muscle/
cd-hit  http://www.bioinformatics.org/cd-hit/