...
| | | 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 | AbySS/1.5.2
pandaseq/2.5
trinity/7.17.14
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/2.15.3
R/3.01
R/3.0.2
R/3.0.3
R/3.1.0
mathematica/8.0
mathematica/8.0.4
mathematica/9.0.0
mathematica/9.0.1
mathematica/10.0.2
matlab/2012b
matlab/2013a*
matlab/2014a
matlab/2014b | | Microbial ecology | QIIME/1.5.0*
QIIME/1.6.0
QIIME/1.7.0
QIIME/1.8.0
QIIME/1.9.0
mothur/1.25.1
mothur/1.29.1 |
| Classification | Module |
|---|
| NGS | BCFtools/1.2 Picard/1.139 CirSeq/3
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
ngsplot
samtools/0.1.18*
samtools/0.1.19 | | Phylogenetics | mrbayes/3.1.2
paml/4.8
PhyML/3.1 | | RNA | ViennaRNA/2.1.6*
mirdeep2/2.0.0.5*
randfold/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
tophat/2.0.13
transdecoder/2.0
trinity/7.17.14 | Statistical Genetics
/GWAS | ancestrymap/6210
fbat/2.0.3
haploview/4.1
impute/2.0.3
mach/1.0.16
merlin/1.1.2
pbat/3.61
pedcheck/1.1
plink/1.06
plinkseq/0.10
vcftools/0.1.12b |
|
Performance Considerations using threads
In general, there are useful performance gains using threads, but it can also be abused by using too many. Applications supporting thread parallelism may have varying degree of internal support.
Application performance is not always well documented and it may be beneficial to you to do some benchmarking. By doing so you will be in a position to better utilize the cluster resources. For example here is a benchmark examination of blastp and other tools.