Tools
|
Module Name
|
Version
|
Note
|
| ABySS 2.0 |
abyss/git-gcc |
2.00 |
|
| Anvio |
intelpython/3.5 |
|
|
| augustus |
augustus/3.3 |
3.30 |
|
| bbmap / bbtool |
bbmap/37.36 |
37.36 |
|
| bbtool |
bbmap/37.36 |
37.36 |
|
| bcftools |
bcftools/1.5 |
1.50 |
|
| bedtools |
bedtools/2.25.0 |
2.25.0 |
|
| bioawk |
bioawk/git-gcc |
|
|
| BioPython |
intelpython/2.7, intelpython/3.5, python/3.4.5, python/3.5.2 |
1.70 |
|
| BLAST |
ncbi-blast/2.6.0 |
2.6.0 |
|
| Bowtie2 |
bowtie2/2.2.9 |
2.2.9 |
|
| bwa |
bwa/0.5.15 |
0.5.15 |
|
| csvkit |
intelpython/2.7, intelpython/3.5, python/3.4.5, python/3.5.2 |
|
|
| ddocent |
|
|
|
| Diamond |
diamond/git |
|
|
| emboss |
emboss/gcc, emboss/6.2.2 |
6.2.2 |
|
| entrez |
entrez/git-gcc |
|
|
| exonerate |
exonerate/2.2.0 |
2.2.0 |
|
| fastqc |
fastqc/v0.11.5 |
0.11.5 |
|
| fastx_toolkit |
fastx_toolkit/0.0.14 |
0.0.14 |
|
| freebayes |
freebayes/git |
|
|
| gatk |
gatk/3.8-0 |
3.8.0 |
|
| GeneMarkET-ES |
GeneMarkET-ES/4.32.0 |
4.32.0 |
|
| GeneMarkSuite |
GeneMarkSuite/4.30.0 |
4.30.0 |
|
| HTSLib |
htslib/git |
1.50 |
|
| IDBA-UD |
idba-ud/git |
|
|
| kentUtils |
kentUtils/git |
|
|
| lastaligner |
lastaligner/719 |
719.00 |
|
| lastz |
lastz/1.03.73 |
1.03.73 |
|
| maker |
maker/2.31.9 |
2.31.9 |
|
| MaSuRCA |
MaSuRCA/3.2.2 |
3.2.2 |
|
| Meraculous2 |
meraculous/v2.2.4 |
2.2.4 |
|
| MultiQC |
module load anaconda2/4.2.0 |
|
|
| MUMmer |
mummer/4.0.0beta1 |
4.0.0 |
|
| ncbi-blast |
ncbi-blast/2.6.0 |
2.6.0 |
|
| nseg |
nseg/gcc |
|
|
| Python |
|
|
|
| Qiime |
module load anaconda2/4.2.0, source activate qiime2-2017.9, source activate qiime1 |
|
|
| Quast |
module load anaconda2/4.2.0 |
4.2.0 |
|
| R |
R/3.3.2 |
3.3.2 |
|
| readseq |
readseq/java |
|
|
| RepeatMasker |
RepeatMasker/4.0.6 RepeatMasker/4.0.7 |
4.0.6, 4.0.7 |
|
| RepeatScout |
RepeatScout/1.0.5 |
1.0.5 |
|
| Samtools |
samtools/git |
|
|
| seqkit |
seqkit/0.7.1 |
0.7.1 |
|
| seqtk |
seqtk/git |
|
|
| skewer |
skewer/git |
|
|
| snap |
snap/0.15.4 |
0.15.4 |
|
| SOAPdenovo |
SOAPdenovo2/git |
|
|
| Space |
sspace/basic |
|
|
| Spades |
SPAdes/3.11.0 |
3.11.0 |
|
| SRA Tools |
sra-tools/git |
|
|
| Stacks |
stacks/1.47 |
|
|
| SubRead |
subread/1.5.1-source |
|
|
| Taxon Kit |
taxonkit/gcc |
|
|
| taxonkit |
taxonkit/gcc |
|
|
| TopHat |
tophat/2.1.1 |
|
|
| trf |
trf/409 |
|
|
| trim galore |
TrimGalore/0.4.3 |
|
|
| Trimmomatic |
trimmomatic/0.36 |
|
|
| Tuxedo suit (= Bowtie2, TopHat, Cufflink) |
cufflinks/2.2.1 |
|
|
| vcf tools |
vcftools/0.1.13 |
|
|
| velvet |
velvet/1.2.10 velvet/1.2.10-301kmer-openmp |
|
|
