...
export BOWTIE2_INDEXES=/cluster/tufts/genomes/MusMusculus/mm10/Sequence/Bowtie2Index
export MYDATADIR=/cluster/shared/myutln/mmdata
bowtie2 -q -x genome -1 $MYDATADIR/myreads_1.fq -2 $MYDATADIR/myreads_2.fq -S myreads.sam
d. HPC Modules for Bioinformatics
To list the entirety of the module collection use this command
module avail
To load a module use this command
module load modulename/version
as listed below. Default settings are annotated by '*'
module list shows currently loaded modules.
To unload a module use this command
module unload modulename/version
| | | Classification | Module |
|---|
| Align/Mapping | blast/2.2.24
blat/20140708
bowtie/0.12.7*
bowtie/1.0.1
bowtie/2.1.0
bowtie2/2.2.3*
bwa/0.7.9a
exonerate/2.2.0 | | Assembly | pandaseq/2.5
velvet/1.0.19
velvet/1.2.03
velvet/1.2.10 | | BioVisual | cytoscape/2.8.3
IGV/1.5.30
| | ChIP-Seq | MACS/1.4.2-1
MAnorm/2014-04-03 | | General Purpose | R/2.10.1
R/2.15.0*
R/2.15.2
R/2.15.3
R/3.01
R/3.0.2
R/3.0.3
R/3.1.0
mathematica/8.0
mathematica/8.04
mathematica/9.0.0
mathematica/9.0.1
matlab/2011b
matlab/2012a
matlab/2012b
matlab/2013a*
matlab/2014a
| | Microbial ecology | QIIME/1.5.0*
QIIME/1.6.0
QIIME/1.7.0
QIIME/1.8.0
mothur/1.25.1
mothur/1.29.1 |
| Classification | Module |
|---|
| NGS | GATK/3.1-1
HTseq/0.5.4a*
HTseq/0.6.1p1
IGV/1.5.30
bedtools/2.17.0*
bedtools/2.19.1
bowtie/0.12.7*
bowtie/1.0.1
bowtie/2.1.0
bowtie/2.2.3*
bwa/0.7.9a
fastx/0.0.13
samtools/0.1.18*
samtools/0.1.19 | | Phylogenetics | mrbayes/3.1.2 | | RNA | ViennaRNA/2.1.6*
mirdeep2/2.0.0.5*
ranfold/2/0* | | RNA-Seq | STAR/2.30e*
cufflinks/0.8.3
cufflinks/2.0.0
cuffinks/2.0.2*
cufflinks/2.1.1
misopy/0.5.2
rsem/1.2.4
tablemaker/2.1.1*
tophat/1/0/14
tophat/2.0.9*
tophat/2.0.10 | Statistical Genomics
/GWAS | ancestrymap/6210
haploview/4.1
impute/2.0.3
mach/1..0.16
merlin/1.1.2
pbat/3.61
pedcheck/1.1
plink/1.06 |
|