Bioinformatics Modules

The Canadian Centre for Computational Genomics (C3G) in partnership with the Alliance Canada, allows researchers to access hundreds of bioinformatics tools and modules pre-installed on several HPC centres including Rorqual, Nibi, Fir, Trillium and Narval.

Use the following command to explore the available tools:

user@machine:~$ module avail mugqic/
Available Modules

Module Name

Version(s)

3DChromatin_ReplicateQC:

1.0.1

ABySS:

1.3.5

2.0.2

Accurity:

32acfd1e-debug

AffymetrixApt:

1.18.0

1.19.0

1.20.5

AGE:

master-20181210

AGeNT:

2.0.5

3.0.6

amber:

3.5

3.9

4.0

AMOS:

3.1.0

anaconda:

N/A

AnnotSV:

3.4.4

anvio:

7.1

apptainer:

1.3.6

arriba:

2.1.0

2.3.0

ARTIC:

1.2.1

ASCAT:

2.3

aspera-connect:

3.3.3

Athena:

1.0

autoconf:

2.69

bambam:

1.4

BAMixChecker:

1.0.1

bamtools:

2.4.1

2.5.1

Basecall_T7_GPU:

1.4.11.57

1.4.20.71

1.4.2.47

bash:

4.4.18

BBMap:

38.90

bcbio.variation:

0.2.6

bcbio.variation.recall:

0.1.7

0.2.6

bcftools:

1.10.2

1.11

1.12

1.14

1.15

1.19

1.2

1.3

1.6

1.8

1.9

beagle:

03May16.862

r1399

bedops:

v2.4.28

v2.4.35

v2.4.40

bedtools:

2.17.0

2.22.1

2.25.0

2.26.0

2.27.0

2.29.2

2.30.0

bioinfokit:

1.0.5

bio-playground:

master

bismark:

0.16.1

0.16.3

0.17.0

0.18.1

0.18.2

0.21.0

0.23.1

BisSNP:

0.82.2

1.0.0

blast:

2.10.0+

2.11.0+

2.13.0+

2.2.29+

2.3.0+

2.7.1+

2.9.0+

boost:

1.63.0

1.66.0

bowtie:

1.0.0

1.1.2

1.2.0

1.2.2

1.3.1

bowtie2:

2.2.3

2.2.4

2.2.9

2.3.0

2.3.1

2.3.5

breakdancer:

1.1_2011_02_21

breakseq2:

2.2

BSMAPz:

1.1.3

butter:

0.3.3

bvatools:

1.3

1.4

1.5

1.6

bwa:

0.7.10

0.7.12

0.7.15

0.7.17

0.7.18

bwakit:

0.7.12

0.7.15

bwa-mem2:

2.2.1

Canu:

1.5

CASPER:

0.8.2

cd-hit:

4.5.4-2011-03-07

cellranger:

1.3.0

1.3.1

2.0.0

2.0.2

2.1.1

3.0.0

3.0.1

3.0.2

3.1.0

4.0.0

5.0.1

6.0.2

6.1.1

7.0.1

8.0.1

9.0.1

cellranger-arc:

1.0.1

2.0.0

cellranger-atac:

1.0.0

1.0.1

1.1.0

2.0.0

cellranger-dna:

1.0.0

CheckM:

1.2.1

chicago:

1.1.5

1.19.0

ChromImpute:

1.0.3

circos:

0.69-6

circos-tools:

0.23

Clair3:

1.0.10

1.1.0

CNVkit:

0.9.5

0.9.9

cobalt:

1.11

1.13

1.16

Conpair:

0.1

0.2

0.2.1

CoVSeQ_tools:

1.0.0

1.1.0

1.1.1

1.2.0

1.2.1

1.2.2

cpsr:

0.6.2

CrossMap:

0.5.2

CTPR:

1.1

cufflinks:

2.2.1

cutadapt:

2.10

2.9

deepTools:

2.4.2

2.5.0.1

2.5.3

3.3.1

3.5.0

3.5.1

3.5.4

deepvariant:

1.8.0

Delly:

0.7.7

0.7.8

0.7.9

0.8.1

demuxlet:

master_20190913

master_20210204

diamond:

2.1.4

djerba:

1.8.0

dorado:

0.5.3

0.9.1

DOvEE_genpipes:

4.3.2

4.3.3

dragmap:

1.2.1

1.3.0

duk:

1.1

duphold:

0.1.1

dysgu:

1.7.0

ea-utils:

1.1.2-537

emboss:

6.4.0

6.6.0

EPACTS:

3.2.6

exonerate:

2.2.0

ExpansionHunterDenovo:

0.8.7

0.9.0

export2graphlan:

0.22

fastp:

0.19.7

0.23.2

0.23.4

fastqc:

0.11.2

0.11.5

0.11.6.devel

0.11.9

0.12.1

FastQValidator:

0.1.1a

FastTree:

2.1.10

2.1.7

fastx:

0.0.14

fgbio:

0.6.1

0.7.0

1.1.0

1.3.0

1.4.0

2.1.0

FLASH:

1.2.11

1.2.8

fqtrim:

0.9.7

freebayes:

1.2.0

1.3.4

FusionCatcher:

0.99.7b

1.33

GangSTR:

2.4.4

gcc:

4.9.3

gcta:

1.92.4beta

gemBS:

3.3.0

gemBS-rs:

4.0.4

gemini:

0.18.0

0.18.2

0.18.3

0.19.1

0.20.1

0.30.2

gemLibrary:

v1.315

GenAP_Pipes:

3.0.0

GenomeAnalysisTK:

3.2-2

3.3-0

3.5

3.6

3.7

3.8

4.0.10.1

4.0.11.0

4.0.2.1

4.0.8.1

4.1.0.0

4.1.1.0

4.1.2.0

4.1.8.1

4.2.2.0

4.2.6.1

4.4.0.0

4.6.0.0

GenomeTools:

1.5.9

genpipes:

3.0.0

3.1.0

3.1.1

3.1.2

3.1.4

3.1.5

3.2.0

3.3.0

3.4.0

3.5.0

3.6.0

3.6.1

3.6.2

4.0.0

4.1.0

4.1.1

4.1.2

4.2.0

4.3.0

4.3.1

4.3.2

4.4.0

4.4.1

4.4.2

4.4.3

4.4.4

4.4.5

4.5.0

4.6.0

4.6.1

5.0.1

5.0.2

5.0.3

5.1.0

6.0.0

covid_1.0

gget:

0.27.2

ghostscript:

8.70

glances:

3.2.3.1

globus-cli:

3.24.0

3.7.0

gnuplot:

4.6.4

4.6.6

GraPhlAn:

1.1.3

gridss:

2.13.2

gripss:

2.3.1

gsort:

0.0.6

0.1.4

gsutil:

4.61

gtex-pipeline:

master-9b381b7

master-edc2794

guppy:

gpu-4.0.11

gpu-4.2.2

gpu-4.4.0

gpu-4.5.2

gpu-6.5.7

Hclust2:

1.0.0

hcp_tools:

1.2.5R_11

HDF5:

1.8.20

HiCPlotter:

v0.7.3

hicpro:

2.11.1

hicup:

v0.5.9

v0.7.0

HiCUP:

0.8.3

v0.5.9

v0.7.0

v0.7.2

HiFiCNV:

1.0.1

HiPhase:

1.4.5

hmmcopy_utils:

master-29a8d1d

hmmer:

2.3.2

3.1b1

3.1b2

3.3.2

homer:

4.11

4.7

4.9.1

5.1

htseq:

2.0.4

htslib:

1.10.2

1.11

1.12

1.14

1.16

1.19.1

1.2.1

1.3

1.4.1

1.8

1.9

ichorCNA:

0.2.0

0.4.0

master-5bfc03e

idba:

1.1.3g1

igv:

2.11.9

2.3.23

igvtools:

2.11.9

2.3.14

2.3.67

ImageMagick:

7.1.0-4

infernal:

1.1.4

InterOp:

1.1.1

ivar:

1.2.1

1.2.2

1.2.3

1.3

JAGS:

4.3.0

java:

openjdk-jdk-11.0.2

openjdk-jdk1.6.0_38

openjdk-jdk-17.0.1

openjdk-jdk1.7.0_60

openjdk-jdk1.8.0_72

openjdk-jdk-19.0.1

jellyfish:

2.1.3

2.2.6

2.3.0

juicer:

0.7.0

1.11.09

kaiju:

1.7.3

kallisto:

0.44.0

0.46.1

0.48.0

0.50.0

0.50.1

kentUtils:

302.1.0

kmergenie:

1.5692

knotAnnotSV:

1.1.5

kraken2:

2.0.9-beta

2.1.0

KronaTools:

2.6.1

lapack:

3.5.0

LAST:

959

libStatGen:

1.0.13

linx:

1.22

1.25

lofreq:

2.1.5

longranger:

2.1.2

2.1.3

2.1.4

2.1.6

2.2.2

LUMPY-SV:

0.2.13

master_20190208

MACS:

2.0.10.09132012

MACS2:

2.1.0.20140616

2.1.0.20151222

2.1.1.20160309

2.2.7.1

mafft:

7.310

Manta:

1.5.0

Medaka:

1.0.3

MeFiT:

2015-07-31

MELT:

2.1.4

2.1.5

metacherchant:

0.1.0

MetaSV:

0.5.4

0.5.5

MetaWRAP:

1.3

miniconda2:

N/A

miniconda3:

N/A

minimap2:

2.17

2.28

mirdeep2:

0.0.5

0.0.8

0.1.3

MiXCR:

3.0.5

modkit:

0.2.6

0.4.3

mosdepth:

0.2.4

0.3.3

0.3.4

mpich:

3.1.4

mugqic_pipelines:

2.0.1

2.0.2

2.1.0

2.1.1

2.2.0

2.2.1

2.3.0

mugqic_R_packages:

1.0.1

1.0.2

1.0.3

1.0.4

1.0.5

1.0.6

1.0.7

mugqic_tools:

1.10.4

2.0.2

2.0.3

2.1.0

2.10.0

2.10.10

2.10.2

2.10.3

2.10.4

2.10.5

2.10.6

2.10.7

2.10.8

2.10.9

2.1.1

2.1.10

2.11.0

2.1.11

2.11.1

2.1.12

2.11.2

2.11.3

2.12.0

2.12.1

2.12.2

2.12.3

2.12.4

2.12.5

2.12.6

2.12.7

2.12.8

2.12.9

2.1.3

2.1.4

2.1.5

2.1.6

2.1.7

2.1.8

2.1.9

2.2.0

2.2.1

2.2.2

2.2.3

2.2.4

2.3.0

2.3.1

2.3.2

2.4.0

2.5.0

2.6.0

2.6.1

2.7.0

2.8.0

2.8.1

2.8.2

2.9.0

2.9.1

MultiQC:

1.10.1

1.12

1.14

1.20

1.22.2

1.23

1.25.1

1.7

1.8

1.9

v1.3dev

v1.6

MUMmer:

3.23

MUSCLE:

3.8.31

mutect:

1.1.6

NanoGLADIATOR:

1.0

NanoPlot:

1.42.0

Nanopolish:

0.11.1

0.13.3

ncov-random-scripts:

20210415

ncov-tools:

1.6

1.8

20200820

nextclip:

b833dd9

nextflow:

22.10.6

Nextstrain:

2.33

NGSCheckMate:

1.0.0

1.0.0_rjme

Octopus:

0.6.2-beta

olink-ngs2counts:

5.1.0

oncokb-annotator:

3.4.1

OpenBLAS:

0.2.14

0.2.17

0.2.20

OpenMPI:

4.0.0

openssl:

1.1.0

1.1.0e

pandoc:

1.13.1

1.15.2

2.16.1

2.16.2

parallel:

20130822

20170322

20210922

parallel-fastq-dump:

0.6.5

Pascal:

20191025

pave:

1.6

1.7.1

pbccs:

6.4.0

pbmm2:

1.16.99

pbs-drmaa:

1.0.18

PBSuite:

15.2.20beta

pcgr:

0.9.2

1.0.3

1.2.0

1.4.1

2.0.3

2.1.2

perl:

5.18.2

5.22.1

5.34.0

5.40.1

picard:

1.118

1.123

2.0.1

2.10.7

2.17.3

2.23.3

2.26.6

2.27.4

2.9.0

pigz:

2.3

2.4

pipeline:

1.3

Platypus:

0.8.1

popoolation2:

1201

prinseq-lite:

0.20.3

0.20.4

prodigal:

2.6.3

Prokka:

1.12

purple:

2.53

3.4.1

3.7.1

4.0.1

pycoQC:

2.5.2

python:

2.7.10_qiime

2.7.11

2.7.12

2.7.13

2.7.14

2.7.16

2.7.16_LDSC

2.7.18

2.7.8

3.10.1

3.10.2

3.10.4

3.11.1

3.12.2

3.4.0

3.4.8

3.5.2

3.5.5

3.6.5

3.7.3

3.8.5

3.9.1

QT:

4.8.7

qualimap:

2.2.1

2.2.2dev

Quast:

5.0.2

RAPSearch2:

2.12

2.24

ray:

2.3.1

R_Bioconductor:

3.1.2_3.0

3.2.3_3.2

3.3.0_3.4

3.3.2_3.4

3.3.3_3.4

3.4.1_3.5

3.4.2_3.6

3.4.3_3.6

3.4.4_3.6

3.5.0_3.7

3.5.1_3.7

3.5.3_3.8

3.6.0_3.9

3.6.1_3.10

3.6.3_3.11

4.0.3_3.12

4.1.0_3.13

4.2.1_3.15

4.2.2_3.16

4.3.2_3.18

RepeatMasker:

4.0.7

rnammer:

1.2

rnaseqc:

1.1.7

1.1.8

2.4.2

RNAsnp:

1.2

rsem:

1.2.12

1.3.1

1.3.3

RSeQC:

4.0.0

Ruby:

2.5.3

3.1.0

rust:

1.61.0

1.75.0

salmon:

1.3.0

1.5.1

1.6.0

sambamba:

0.6.5

0.6.6

0.6.8

0.7.0

0.8.0

0.8.1

0.8.2

samblaster:

0.1.24

samtools:

0.1.19

1.0

1.10

1.11

1.12

1.14

1.19.2

1.2

1.3

1.3.1

1.4

1.4.1

1.9

sawfish:

0.12.9

scalpel:

0.3.2

0.5.2

SCoNEs:

2.1.1

2.1.2

seq2fun:

1.2.2

1.2.5

seqkit:

2.5.0

SeqKit:

0.11.0

seqtk:

1.0

1.0-r82b

1.2

Sequenza-utils:

3.0.0

ShortStack:

3.3

signalp:

4.1

6.0h

simple_sv_annotation:

1.0.0

skewer:

0.2.2

Smoove:

0.2.2

0.2.3

smrtanalysis:

2.3.0.140936.p1

2.3.0.140936.p2

2.3.0.140936.p4

2.3.0.140936.p5

SMRTLink:

10.1.0

11.0.0

12.0.0

5.1.0

6.0.0

7.0.0

8.0.0

9.0.0

snap:

0.15

1.0beta.18

2013-11-29

snpEff:

3.6

4.0

4.2

4.3

4.5covid19

5.1

sortmerna:

4.3.6

SPAdes:

3.10.0

3.13.0

3.7.1

sparsehash:

2.0.3

sphinx:

master

SplAdder:

1.0.0

sratoolkit:

2.10.5

2.6.2

2.8.2-1

Stacks:

1.46

2.55

star:

2.4.0f1

2.5.0c

2.5.1b

2.5.2a

2.5.2b

2.5.3a

2.5.4b

2.7.10a

2.7.2b

2.7.3a

2.7.8a

STAR-Fusion:

1.10.0

1.10.1

1.14.0

1.8.1

Strelka2:

2.9.10

StringTie:

1.3.5

2.1.4

strkit:

0.21.0

supernova:

1.1.4

1.1.5

1.2.0

1.2.2

2.0.1

2.1.1

SURPI:

1.0.18

SvABA:

0.2.1

0.2.2-beta

1.1.0

svim:

2.0.0

sv-prep:

1.0.1

SVTyper:

0.7.0

tabix:

0.2.6

tclsh:

8.6ubuntu2404

TELR:

1.0

TelSeq:

0.0.2

tmhmm:

2.0c

tools:

1.10.4

tophat:

2.0.13

2.0.14

2.1.1

TransDecoder:

2.0.1

5.7.0

TRF:

4.09

trgt:

1.4.1

trimmomatic:

0.32

0.35

0.36

0.39

trinity:

20140413p1

2.0.4

2.0.4_patch

2.1.1

2.15.1

2.2.0

2.2.0_patch

2.8.6

trinotate:

2.0.1

20131110

2.0.2

4.0.0

4.0.2

ucsc:

20140212

v326

v346

v359

v387

usearch:

10.0.240

11.0.667

5.2.236

8.1.1861

validatefastq:

0.1.1

VarDictJava:

1.4.10

1.4.8

1.4.9

1.8.2

1.8.3

variantbam:

1.4.3

VarScan:

2.3.9

2.4.2

2.4.3

2.4.4

vawk:

0.0.2

vcf2db:

master_20180427

master.c391574_20210730

vcfanno:

0.2.9

0.3.2

0.3.3

vcflib:

1.0.0

1.0.1

vcftools:

0.1.11

0.1.14

velvet:

1.2.10

verifyBamID:

1.1.3

2.0.1

devMaster_20151216

vg:

1.28.0

ViennaRNA:

2.3.3

2.4.14

VIP:

1.0.1

viromatch:

master44edca0

vsearch:

1.11.1

vt:

0.57

weblogo:

2.8.2

3.3

3.5.0

wgs-assembler:

8.1

WHAM:

1.8.0

wkhtmltopdf:

0.12.6

wub:

0.5.1

zlib:

1.2.11

Last updated: 2025-04-18 16:18:43 UTC

Use the following command to load any of the available tools:

# module add mugqic/<tool>/<version>
user@machine:~$ module add mugqic/samtools/1.4.1

# Now samtools 1.4.1 is available to use. To check:
user@machine:~$ samtools

Use the following command to check available GenPipes versions pre-installed on the server:

user@machine:~$ module avail genpipes