GDC software stack

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Revision as of 14:49, 13 January 2022 by Sfux (talk | contribs) (Available tools and libraries (new software stack))

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GDC

The Genetic Diversity Centre (GDC) of ETH Zurich is a well established knowledge and technology platform of the D-USYS Department. It offers a well equipped user-lab and customised bioinformatic support and services for research related to genetic and genomic diversity in a wide range of organisms. It offers customized support for research projects in the field of genetic diversity with a wide range of technical expertise and a dynamic, well-connected team. The GDC is open to all academic institutions within Switzerland.

Contact

Genetic Diversity Centre
Universitätstrasse 16
CHN E 55.1
8092 Zurich / Switzerland
http://www.gdc.ethz.ch

Software stack on Euler

The GDC bioninformatics software stack on Euler was installed as part of GDCs SIS subscription. It is a collection of tools and libraries, selected by the GDC team. The GDC team builds runscripts and workflows based on the tools of this software stack. The tools are available to all cluster users, but if you are interested in runscripts or workflows, then please contact the GDC team.

Please note that the GDC software stack is part of the old Euler software stack and can not be used together with tools from the new software stack.

Old vs. new software stack

Please note that the GDC software stack was setup as part of the old Euler software stack. Meanwhile, a newer software stack is provided. You can switch back and forth between the old and the new software stack within the current terminal, but you cannot mix tools from both software stacks. There is also the option of setting a permanent default for the software stack that is initialized upon login. You can change this default at any time.

Available tools and libraries (old software stack)

Application Module load command
adapterremoval/2.1.7 module load gcc/4.8.2 gdc adapterremoval/2.1.7
admixtools/4.1 module load gcc/4.8.2 gdc openblas/0.2.13_seq perl/5.18.4 admixtools/4.1
allmaps/d0f2efd module load gcc/4.8.2 gdc python/2.7.11 allmaps/d0f2efd
amrfinderplus/3.9.8 module load gcc/4.8.2 gdc hmmer/3.1 blast/2.9.0 amrfinderplus/3.9.8
angsd/0.912 module load gcc/4.8.2 gdc angsd/0.912
angsd/0.917 module load gcc/4.8.2 gdc angsd/0.917
angsd/0.919 module load gcc/4.8.2 gdc angsd/0.919
angsd/0.925 module load gcc/4.8.2 gdc angsd/0.925
angsd/0.933 module load gcc/4.8.2 gdc angsd/0.933
armadillo/9.700.2 module load gcc/4.8.2 gdc openblas/0.2.13_seq armadillo/9.700.2
atlas/10092019 module load gcc/4.8.2 gdc openblas/0.2.13_seq armadillo/9.700.2 atlas/10092019
atlas/30102020 module load gcc/4.8.2 gdc openblas/0.2.13_seq armadillo/9.700.2 atlas/30102020
augustus/3.2.1 module load gcc/4.8.2 gdc boost/1.55.0 sqlite3/3.11 gsl/1.16 perl/5.18.4 bamtools/2.4.0 suitesparse/4.5.1 openblas/0.2.13_seq augustus/3.2.1
augustus/3.3.2 module load gcc/4.8.2 gdc boost/1.55.0 sqlite3/3.11 gsl/1.16 perl/5.18.4 bamtools/2.5.1 suitesparse/4.5.1 openblas/0.2.13_seq augustus/3.3.2
bamtools/2.4.0 module load gcc/4.8.2 gdc bamtools/2.4.0
bamtools/2.5.1 module load gcc/4.8.2 gdc bamtools/2.5.1
bamutil/1.0.14 module load gcc/4.8.2 gdc bamutil/1.0.14
bayescan/2.1 module load gcc/4.8.2 gdc bayescan/2.1 bayescan/2.1
bbmap/35.85 module load gcc/4.8.2 gdc java/1.8.0_73 bbmap/35.85
bbmap/38.49 module load gcc/4.8.2 gdc java/1.8.0_73 bbmap/38.49
bbmap/38.87 module load gcc/4.8.2 gdc java/1.8.0_73 bbmap/38.87
bcl2fastq/2.19.1 module load gcc/4.8.2 gdc boost/1.55.0 bcl2fastq/2.19.1
beagle/3.3.2 module load gcc/4.8.2 gdc java/1.8.0_73 beagle/3.3.2
beagle/4.1 module load gcc/4.8.2 gdc java/1.8.0_73 beagle/4.1
beast2/2.4.6 module load gcc/4.8.2 gdc java/1.8.0_101 beast2/2.4.6
bedops/2.4.36 module load gcc/4.8.2 gdc bedops/2.4.36
bedtools/2.25 module load gcc/4.8.2 gdc bedtools/2.25
bedtools/2.27.1 module load gcc/4.8.2 gdc bedtools/2.27.1
bedtools/2.28.0 module load gcc/4.8.2 gdc bedtools/2.28.0
bfc/1.0 module load gcc/4.8.2 gdc bfc/1.0
bioconductor/3.1 module load gcc/4.8.2 gdc openblas/0.2.13_seq bioconductor/3.1
bioconductor/3.4 module load gcc/4.8.2 gdc openblas/0.2.13_seq bzip2/1.0.6 zlib/1.2.8 xz/5.2.2 pcre/8.38 curl/7.51 bioconductor/3.4
biojava/4.1.0 module load gcc/4.8.2 gdc java/1.8.0_73 biojava/4.1.0
bismark/0.19.0 module load gcc/4.8.2 gdc perl/5.18.4 bowtie2/2.3.2 samtools/1.3 bismark/0.19.0
blasr/5.3 module load gcc/4.8.2 gdc hdf5/1.8.12 blasr/5.3
blasr_bam/5.3 module load gcc/4.8.2 gdc hdf5/1.8.12 python/2.7.11 perl/5.18.4 samtools/1.3 boost/1.63.0 blasr_bam/5.3
blast/2.3.0 module load gcc/4.8.2 gdc blast/2.3.0
blast/2.9.0 module load gcc/4.8.2 gdc blast/2.9.0
blat/35 module load gcc/4.8.2 gdc blat/35
blobtools/0.9.19.5 module load gcc/4.8.2 gdc python/2.7.11 perl/5.18.4 samtools/1.3 blobtools/0.9.19.5
blobtools/1.1.1 module load gcc/4.8.2 gdc python/3.6.1 perl/5.18.4 samtools/1.3 blobtools/1.1.1
boost/1.55.0 module load gcc/4.8.2 gdc boost/1.55.0
boost/1.63.0 module load gcc/4.8.2 gdc boost/1.63.0
bowtie/1.1.2 module load gcc/4.8.2 gdc bowtie/1.1.2
bowtie2/2.2.6 module load gcc/4.8.2 gdc bowtie2/2.2.6
bowtie2/2.3.0 module load gcc/4.8.2 gdc bowtie2/2.3.0
bowtie2/2.3.2 module load gcc/4.8.2 gdc bowtie2/2.3.2
bowtie2/2.3.4.2 module load gcc/4.8.2 gdc zlib/1.2.8 bowtie2/2.3.4.2
braker/2.1.2 module load gcc/4.8.2 gdc boost/1.55.0 sqlite3/3.11 gsl/1.16 perl/5.18.4 bamtools/2.5.1 suitesparse/4.5.1 openblas/0.2.13_seq augustus/3.3.2 genemark/4.46 samtools/1.7 genomethreader/1.7.1 blast/2.3.0 exonerate/2.4.0 braker/2.1.2
breseq/0.27.1 module load gcc/4.8.2 gdc bowtie2/2.2.6 bioconductor/3.1 breseq/0.27.1
breseq/0.29.0 module load gcc/4.8.2 gdc bowtie2/2.3.0 bioconductor/3.1 breseq/0.29.0
breseq/0.30.1 module load gcc/4.8.2 gdc bowtie2/2.3.2 bioconductor/3.1 breseq/0.30.1
breseq/0.32.0 module load gcc/4.9.2 gdc bowtie2/2.3.2 bzip2/1.0.6 zlib/1.2.8 xz/5.2.2 pcre/8.38 curl/7.51 bioconductor/3.4 breseq/0.32.0
breseq/0.34.1 module load gcc/4.9.2 gdc bowtie2/2.3.2 bzip2/1.0.6 zlib/1.2.8 xz/5.2.2 pcre/8.38 curl/7.51 bioconductor/3.4 breseq/0.34.1
breseq/0.35.5 module load gcc/4.9.2 gdc bowtie2/2.3.2 bzip2/1.0.6 zlib/1.2.8 xz/5.2.2 pcre/8.38 curl/7.51 bioconductor/3.4 breseq/0.35.5
busco/1.1b1 module load gcc/4.8.2 gdc python/3.4.3 blast/2.3.0 hmmer/3.1 boost/1.55.0 sqlite3/3.11 gsl/1.16 suitesparse/4.5.1 bamtools/2.4.0 augustus/3.2.1 emboss/6.5.7 busco/1.1b1
busco/2.0 module load gcc/4.8.2 gdc python/3.4.3 blast/2.3.0 hmmer/3.1 boost/1.55.0 sqlite3/3.11 gsl/1.16 suitesparse/4.5.1 bamtools/2.4.0 augustus/3.2.1 emboss/6.5.7 busco/2.0
busco/3.0.2 module load gcc/4.8.2 gdc python/3.6.1 blast/2.3.0 hmmer/3.1 boost/1.55.0 sqlite3/3.11 gsl/1.16 suitesparse/4.5.1 bamtools/2.4.0 augustus/3.2.1 emboss/6.5.7 busco/3.0.2
bwa/0.7.12 module load gcc/4.8.2 gdc bwa/0.7.12
bwa/0.7.17 module load gcc/4.8.2 gdc bwa/0.7.17
bzip2/1.0.6 module load gcc/4.8.2 gdc bzip2/1.0.6
canu/1.6 module load gcc/4.8.2 gdc perl/5.18.4 java/1.8.0_101 canu/1.6
canu/1.7.1 module load gcc/4.8.2 gdc perl/5.18.4 java/1.8.0_101 canu/1.7.1
cd-hit/4.6.4 module load gcc/4.8.2 gdc perl/5.18.4 cd-hit/4.6.4
cd-hit/4.6.5 module load gcc/4.8.2 gdc perl/5.18.4 cd-hit/4.6.5
cd-hit/4.6.6 module load gcc/4.8.2 gdc perl/5.18.4 cd-hit/4.6.6
cd-hit/4.8.1 module load gcc/4.8.2 gdc perl/5.18.4 cd-hit/4.8.1
circos/0.69-6 module load gcc/4.8.2 gdc perl/5.18.4 circos/0.69-6
clustalw/2.1 module load gcc/4.8.2 gdc clustalw/2.1
cmake/3.15.3 module load gcc/4.8.2 gdc cmake/3.15.3
cmake/3.9.0 module load gcc/4.8.2 gdc cmake/3.9.0
crisp/05032017 module load gcc/4.8.2 gdc perl/5.18.4 python/2.7.11 crisp/05032017
curl/7.51 module load gcc/4.8.2 gdc curl/7.51
defusion/no_version module load new gcc/4.8.2 gdc open_mpi/1.6.5 python/2.7.11 perl/5.18.4 blast/2.3.0 snap/2006-07-28 genemark_es/4 hmmer/3.1 rmblast/2.2.28 repeatmasker/4.0.6 boost/1.55.0 sqlite3/3.11 gsl/1.16 bamtools/2.4.0 suitesparse/4.5.1 openblas/0.2.13_seq augustus/3.2.1 maker/2.31.9 defusion/no_version
diamond/0.9.22 module load gcc/4.8.2 gdc diamond/0.9.22
diamond/0.9.24 module load gcc/4.8.2 gdc diamond/0.9.24
diamond/0.9.28 module load gcc/4.8.2 gdc diamond/0.9.28
diamond/0.9.3 module load gcc/4.8.2 gdc diamond/0.9.3
docent/2.12 module load gcc/4.8.2 gdc python/2.7.11 java/1.8.0_73 perl/5.18.4 freebayes/0.9.20 trimmomatic/0.35 bwa/0.7.12 cd-hit/4.6.4 bedtools/2.25 vcflib/1.0.0 docent/2.12
eigen/3.2.10 module load gcc/6.3.0 gdc eigen/3.2.10
emboss/6.5.7 module load gcc/4.8.2 gdc emboss/6.5.7
epiteome/1.0 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.7 bedtools/2.27.1 segemehl/0.2.0 python/2.7.11 epiteome/1.0
examl/3.0.17 module load gcc/4.8.2 gdc open_mpi/1.6.5 examl/3.0.17
exonerate/2.4.0 module load gcc/4.8.2 gdc exonerate/2.4.0
falcon/1.8.8 module load gcc/4.8.2 gdc python/2.7.11 falcon/1.8.8
falcon_phase/0.1.0_beta module load gcc/4.8.2 gdc python/3.6.1 bwa/0.7.17 mummer/4.0.0b1 bedtools/2.27.1 perl/5.18.4 samtools/1.8 falcon_phase/0.1.0_beta
fasta/36.3.8e module load gcc/4.8.2 gdc perl/5.18.4 fasta/36.3.8e
fastani/1.33 module load gcc/4.8.2 gdc gsl/1.16 fastani/1.33
fastme/2.1.5 module load gcc/4.8.2 gdc fastme/2.1.5
fastp/0.20.0 module load gcc/4.8.2 gdc fastp/0.20.0
fastqc/0.11.4 module load gcc/4.8.2 gdc java/1.8.0_73 fastqc/0.11.4
fastqscreen/0.9.3 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.3 fastqscreen/0.9.3
faststructure/20160120 module load gcc/4.8.2 gdc gsl/1.16 python/2.7.11 faststructure/20160120
fasttree/2.1.11 module load gcc/4.8.2 gdc fasttree/2.1.11
fastx_toolkit/0.0.14 module load gcc/4.8.2 gdc perl/5.18.4 fastx_toolkit/0.0.14
flappie/1.1.0 module load gcc/4.8.2 gdc openblas/0.2.13_seq hdf5/1.8.12 flappie/1.1.0
flash/1.2.11 module load gcc/4.8.2 gdc flash/1.2.11
fraggenescan/1.3.0 module load gcc/4.8.2 gdc perl/5.18.4 fraggenescan/1.3.0
freebayes/0.9.20 module load gcc/4.8.2 gdc python/2.7.11 freebayes/0.9.20
freebayes/1.0.2 module load gcc/4.8.2 gdc python/2.7.11 freebayes/1.0.2
freebayes/1.1.0-3-g961e5f3 module load gcc/4.8.2 gdc python/2.7.11 freebayes/1.1.0-3-g961e5f3
freebayes/1.3.1 module load gcc/4.8.2 gdc python/2.7.11 freebayes/1.3.1
freebayes/1.3.4 module load gcc/4.8.2 gdc freebayes/1.3.4
gargammel/18102019 module load gcc/4.8.2 gdc gsl/1.16 perl/5.18.4 gargammel/18102019
gatk/3.5 module load gcc/4.8.2 gdc java/1.8.0_73 gatk/3.5
gatk/3.8-1 module load gcc/4.8.2 gdc java/1.8.0_73 gatk/3.8-1
gatk/4.0 module load gcc/4.8.2 gdc java/1.8.0_101 python/3.6.1 gatk/4.0
gatk/4.0.8.1 module load gcc/4.8.2 gdc java/1.8.0_101 python/3.6.1 gatk/4.0.8.1
gatk/4.1.2.0 module load gcc/4.8.2 gdc java/1.8.0_101 python/3.6.1 gatk/4.1.2.0
gemma/0.94 module load gcc/4.8.2 gdc gemma/0.94
gemma/0.98.1 module load new gcc/6.3.0 gdc gsl/1.16_gcc630 eigen/3.2.10 gemma/0.98.1
genemark/4.46 module load gcc/4.8.2 gdc perl/5.18.4 genemark/4.46
genemark_es/4 module load gcc/4.8.2 gdc perl/5.18.4 genemark_es/4
genomemapper/0.4.4 module load gcc/4.8.2 gdc genomemapper/0.4.4
genomethreader/1.7.1 module load gcc/4.8.2 gdc genomethreader/1.7.1
genometools/1.5.9 module load gcc/4.8.2 gdc genometools/1.5.9
genotan/0.1.5 module load gcc/4.8.2 gdc gsl/1.16 genotan/0.1.5
ghostz/1.0.2 module load gcc/4.8.2 gdc ghostz/1.0.2
gmap/20160923 module load gcc/4.8.2 gdc perl/5.18.4 gmap/20160923
graphmap/0.3.0 module load gcc/4.8.2 gdc graphmap/0.3.0
gsl/1.16 module load gcc/4.8.2 gdc gsl/1.16
gsl/1.16_gcc630 module load gcc/6.3.0 gdc gsl/1.16_gcc630
gtdb-tk/1.5.0 module load gcc/4.8.2 gdc prodigal/2.6.3 hmmer/3.3.2 python/3.6.1 pplacer/1.1.alpha19 gsl/1.16 fastani/1.33 fasttree/2.1.11 mash/2.3 gtdb-tk/1.5.0
guppy/2.3.1 module load gcc/4.8.2 gdc guppy/2.3.1
guppy/4.5.4 module load gcc/4.8.2 gdc guppy/4.5.4
halc/1.1 module load gcc/4.8.2 gdc python/2.7.11 hdf5/1.8.12 blasr/5.3 boost/1.63.0 lordec/0.6 halc/1.1
hisat2/2.1.0 module load gcc/4.8.2 gdc python/2.7.11 hisat2/2.1.0
hmmer/3.1 module load gcc/4.8.2 gdc hmmer/3.1
hmmer/3.3.2 module load gcc/4.8.2 gdc hmmer/3.3.2
htslib/1.11 module load gcc/4.8.2 gdc htslib/1.11
hyphy/2.5.1 module load new gcc/4.9.2 gdc open_mpi/3.0.0 hyphy/2.5.1
idba/1.1.1 module load gcc/4.8.2 gdc idba/1.1.1
imr/0.4.1 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.3 java/1.8.0_73 bwa/0.7.12 picard-tools/2.0.1 zlib/1.2.8 imr/0.4.1
instruct/3.2.09 module load gcc/4.8.2 gdc instruct/3.2.09
itsx/1.1.1 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 itsx/1.1.1
itsx/1.1.2 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 itsx/1.1.2
itsx/1.1.3 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 itsx/1.1.3
java/14.0.2 module load gcc/4.8.2 gdc java/14.0.2
java/1.8.0_101 module load gcc/4.8.2 gdc java/1.8.0_101
java/1.8.0_73 module load gcc/4.8.2 gdc java/1.8.0_73
jellyfish/1.1.11 module load gcc/4.8.2 gdc jellyfish/1.1.11
jellyfish/2.2.10 module load gcc/4.8.2 gdc jellyfish/2.2.10
jitterbug/09032016 module load gcc/4.8.2 gdc python/2.7.11 betdools/2.25 jitterbug/09032016
kaiju/1.6.2 module load gcc/4.8.2 gdc python/2.7.11 perl/5.18.4 kaiju/1.6.2
kaiju/1.7.2 module load gcc/4.8.2 gdc python/2.7.11 perl/5.18.4 kaiju/1.7.2
kallisto/0.43.0 module load gcc/4.8.2 gdc hdf5/1.8.12 kallisto/0.43.0
kallisto/0.45.0 module load gcc/4.8.2 gdc hdf5/1.8.12 kallisto/0.45.0
kat/2.3.1 module load gcc/4.8.2 gdc python/3.4.3 boost/1.55.0 kat/2.3.1
kraken/0.10.5 module load gcc/4.8.2 gdc perl/5.18.4 kraken/0.10.5
kraken/master_29072019 module load gcc/4.8.2 gdc perl/5.18.4 kraken/master_29072019
lastz/1.02 module load gcc/4.8.2 gdc python/2.7.11 lastz/1.02
ldhat/2.2a module load gcc/4.8.2 gdc ldhat/2.2a
ldhelmet/1.9 module load gcc/4.8.2 gdc boost/1.63.0 gsl/1.16 ldhelmet/1.9
ldhot/0.4 module load gcc/4.8.2 gdc ldhot/0.4
lfmm/1.4 module load gcc/4.8.2 gdc lfmm/1.4
lofreq/2.1.2 module load gcc/4.8.2 gdc python/2.7.11 lofreq/2.1.2
lordec/0.6 module load gcc/4.8.2 gdc boost/1.63.0 lordec/0.6
lorte/1.2 module load gcc/4.8.2 gdc python/2.7.11 blast/2.3.0 lorte/1.2
ltrfinder/1.0.7 module load gcc/4.8.2 gdc perl/5.18.4 ltrfinder/1.0.7
macse/1.01b module load gcc/4.8.2 gdc java/1.8.0_73 macse/1.01b
mafft/7.273 module load gcc/4.8.2 gdc mafft/7.273
maker/2.31.9 module load gcc/4.8.2 gdc open_mpi/1.6.5 perl/5.18.4 snap/2006-07-28 blast/2.3.0 exonerate/2.4.0 genemark_es/4 hmmer/3.1 rmblast/2.2.28 repeatmasker/4.0.6 boost/1.55.0 sqlite3/3.11 gsl/1.16 bamtools/2.4.0 suitesparse/4.5.1 openblas/0.2.13_seq augustus/3.2.1 maker/2.31.9
mash/2.3 module load gcc/4.8.2 gdc mash/2.3
masurca/3.2.2 module load gcc/4.8.2 gdc perl/5.18.4 boost/1.55.0 masurca/3.2.2
masurca/3.2.3 module load gcc/4.8.2 gdc perl/5.18.4 boost/1.55.0 masurca/3.2.3
masurca/3.2.8 module load gcc/4.8.2 gdc perl/5.18.4 boost/1.55.0 masurca/3.2.8
masurca/3.3.0b module load gcc/4.8.2 gdc perl/5.18.4 boost/1.55.0 masurca/3.3.0b
masurca/3.3.3 module load gcc/4.8.2 gdc perl/5.18.4 boost/1.55.0 masurca/3.3.3
mccortex/1.0.1 module load gcc/4.8.2 gdc perl/5.18.4 python/2.7.11 xz/5.2.2 mccortex/1.0.1
mcl/14.137 module load gcc/4.8.2 gdc mcl/14.137
megahit/1.1.3 module load gcc/4.8.2 gdc python/2.7.11 megahit/1.1.3
megahit/1.2.2_beta module load gcc/4.9.2 gdc python/2.7.11 megahit/1.2.2_beta
megahit/1.2.9 module load gcc/4.9.2 gdc python/2.7.11 megahit/1.2.9
meme/4.12.0 module load gcc/4.8.2 gdc open_mpi/1.6.5 java/1.8.0_91 perl/5.18.4 python/2.7.11 meme/4.12.0
meshclust2/2.3.0 module load new gcc/5.2.0 gdc meshclust2/2.3.0
metabat/2.12.1 module load gcc/4.9.2 gdc boost/1.55.0 python/2.7.11 metabat/2.12.1
metaphlan/2.0 module load gcc/4.8.2 gdc python/2.7.11 bowtie2/2.2.6 metaphlan/2.0
metavelvet/1.2.02 module load gcc/4.8.2 gdc metavelvet/1.2.02
metaxa2/2.2 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 blast/2.3.0 mafft/7.273 usearch/8.1 metaxa2/2.2
metaxa2/2.2.3 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.3.2 blast/2.9.0 mafft/7.273 usearch/11.0.667 metaxa2/2.2.3
methyldackel/0.3.0 module load gcc/4.8.2 gdc methyldackel/0.3.0
migrate/3.6.11 module load gcc/4.8.2 gdc migrate/3.6.11
miniasm/0.2 module load gcc/4.8.2 gdc perl/5.18.4 minimap2/2.2 miniasm/0.2
miniasm/0.3 module load gcc/4.8.2 gdc perl/5.18.4 minimap2/2.12 miniasm/0.3
minimap2/2.12 module load gcc/4.8.2 gdc minimap2/2.12
minimap2/2.17 module load gcc/4.8.2 gdc minimap2/2.17
minimap2/2.2 module load gcc/4.8.2 gdc minimap2/2.2
mmseqs2/3-be8f6 module load gcc/4.8.2 gdc mmseqs2/3-be8f6
mocat/2.0 module load gcc/4.8.2 gdc perl/5.18.4 mocat/2.0
motus/1.1.1 module load gcc/4.8.2 gdc perl/5.18.4 motus/1.1.1
mrbayes/3.2.6 module load gcc/4.8.2 gdc open_mpi/1.6.5 mrbayes/3.2.6
msmc/1.1.0 module load new gcc/4.8.2 gdc dmd/2.080 gsl/1.16 msmc/1.1.0
msmc2/2.1.0 module load new gcc/4.8.2 gdc dmd/2.080 gsl/1.16 msmc2/2.1.0
msmc2/2.1.2 module load new gcc/4.8.2 gdc dmd/2.080 gsl/1.16 msmc2/2.1.2
mummer/4.0.0b1 module load gcc/4.8.2 gdc mummer/4.0.0b1
muscle/3.8.1551 module load gcc/4.8.2 gdc muscle/3.8.1551
nanocall/0.5.13 module load gcc/4.8.2 gdc hdf5/1.8.12 nanocall/0.5.13
nanopolish/0.10.1 module load gcc/4.8.2 gdc perl/5.18.4 python/2.7.11 (or python/3.6.1) nanopolish/0.10.1
ngsep/3.0.2 module load gcc/4.8.2 gdc java/1.8.0_73 ngsep/3.0.2
ngsrelate/0.1 module load gcc/4.8.2 gdc ngsrelate/0.1
ngstools/1.0.1 module load gcc/4.8.2 gdc zlib/1.2.8 gsl/1.16 ngstools/1.0.1
opam/1.2.2 module load gcc/4.8.2 gdc opam/1.2.2
ortho_finder/2.3.11 module load gcc/4.8.2 gdc diamond/0.9.28 mcl/14.137 fastme/2.1.5 mmseqs2/3-be8f6 ortho_finder/2.3.11
pasapipeline/2.0.2 module load gcc/4.8.2 gdc perl/5.18.4 blat/35 gmap/20160923 fasta/36.3.8e pasapipeline/2.0.2
pbmm2/0.4.0 module load new gcc/6.3.0 gdc python/3.6.1 zlib/1.2.8 samtools/1.7 boost/1.63.0 pbmm2/0.4.0
pcangsd/0.8.0 module load gcc/4.8.2 gdc python/2.7.11 pcangsd/0.8.0
pcangsd/0.98 module load gcc/4.8.2 gdc python/3.6.1 pcangsd/0.98
pcre/8.38 module load gcc/4.8.2 gdc pcre/8.38
perl/5.18.4 module load gcc/4.8.2 gdc perl/5.18.4
phyla_amphora/1.0 module load gcc/4.8.2 gdc raxml/8.2.4 hmmer/3.1 emboss/6.5.7 perl/5.18.4 phyla_amphora/1.0
phylosift/1.0.0_01 module load gcc/4.8.2 gdc perl/5.18.4 phylosift/1.0.0_01
picard-tools/1.89 module load gcc/4.8.2 gdc java/1.8.0_73 picard-tools/1.89
picard-tools/2.0.1 module load gcc/4.8.2 gdc java/1.8.0_73 picard-tools/2.0.1
picard-tools/2.20.2 module load gcc/4.8.2 gdc java/1.8.0_73 picard-tools/2.20.2
picard-tools/2.21.3 module load gcc/4.8.2 gdc java/1.8.0_73 picard-tools/2.21.3
picard-tools/2.23.8 module load gcc/4.8.2 gdc java/1.8.0_73 picard-tools/2.23.8
pindel/0.2.5b8 module load gcc/4.8.2 gdc pindel/0.2.5b8
plink/1.07 module load gcc/4.8.2 gdc openblas/0.2.13_seq plink/1.07
plink/1.90 module load gcc/4.8.2 gdc zlib/1.2.8 openblas/0.2.13_seq plink/1.90
popoolation/1.2.2 module load gcc/4.8.2 gdc perl/5.18.4 java/1.8.0_73 bwa/0.7.12 bioconductor/3.1 samtools/1.3 popoolation/1.2.2
popoolation2/1201 module load gcc/4.8.2 gdc perl/5.18.4 java/1.8.0_73 bwa/0.7.12 bioconductor/3.1 samtools/1.3 popoolation2/1201
pplacer/1.1.alpha19 module load gcc/4.8.2 gdc python/2.7.11 pplacer/1.1.alpha19
primer3/2.3.7 module load gcc/4.8.2 gdc perl/5.18.4 primer3/2.3.7
prinseq-lite/0.20.4 module load gcc/4.8.2 gdc perl/5.18.4 prinseq-lite/0.20.4
prodigal/2.6.3 module load gcc/4.8.2 gdc prodigal/2.6.3
prokka/1.11 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 prodigal/2.6.3 java/1.8.0_31 prokka/1.11
prokka/1.13 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 prodigal/2.6.3 java/1.8.0_31 prokka/1.13
prokka/1.14.5 module load gcc/4.8.2 gdc perl/5.18.4 blast/2.9.0 hmmer/3.1 prodigal/2.6.3 java/1.8.0_31 prokka/1.14.5
proovread/2.14.1 module load gcc/4.8.2 gdc perl/5.18.4 blast/2.3.0 samtools/1.3 proovread/2.14.1
python/2.7.11 module load gcc/4.8.2 gdc python/2.7.11
python/3.4.3 module load gcc/4.8.2 gdc python/3.4.3
python/3.6.1 module load gcc/4.8.2 gdc python/3.6.1
python/3.7.4 module load gcc/4.8.2 gdc python/3.7.4
qualimap/2.2.1 module load gcc/4.8.2 gdc java/1.8.0_101 openblas/0.2.13_seq bzip2/1.0.6 zlib/1.2.8 xz/5.2.2 pcre/8.38 curl/7.51 bioconductor/3.4 qualimap/2.2.1
quast/4.5 module load gcc/4.8.2 gdc python/2.7.11 quast/4.5
quast/5.1.0_rc1 module load gcc/4.8.2 gdc python/3.6.1 perl/5.18.4 quast/5.1.0_rc1
quickmerge/0.2 module load gcc/4.8.2 gdc python/2.7.11 quickmerge/0.2
racon/0.5.0 module load gcc/4.8.2 gdc python/2.7.11 racon/0.5.0
racon/1.3.1 module load gcc/4.8.2 gdc python/2.7.11 racon/1.3.1
rad_haplotyper/1.1.5 module load gcc/4.8.2 gdc perl/5.18.4 rad_haplotyper/1.1.5
rad_haplotyper/1.1.9 module load gcc/4.8.2 gdc perl/5.18.4 rad_haplotyper/1.1.9
raxml/8.2.12 module load gcc/4.8.2 gdc open_mpi/1.6.5 raxml/8.2.12
raxml/8.2.4 module load gcc/4.8.2 gdc raxml/8.2.4
raxml-ng/0.1.0rc module load gcc/4.8.2 gdc open_mpi/1.6.5 raxml-ng/0.1.0rc
raxml-ng/1.0.1 module load new gcc/6.3.0 gdc open_mpi/1.6.5 raxml-ng/1.0.1
reads2snp/2.0 module load gcc/4.8.2 gdc reads2snp/2.0
redundans/0.13c module load gcc/4.8.2 gdc perl/5.18.4 python/2.7.11 zlib/1.2.8 redundans/0.13c
repeatmasker/4.0.6 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 rmblast/2.2.28 repeatmasker/4.0.6
repeatmasker/4.0.6_pub module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 rmblast/2.6.0 repeatmasker/4.0.6_pub
repeatmasker/4.0.7 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 rmblast/2.6.0 repeatmasker/4.0.7
repeatmodeler/1.0.11 module load gcc/4.8.2 gdc perl/5.18.4 hmmer/3.1 rmblast/2.2.28 repeatmasker/4.0.6 repeatmodeler/1.0.11
ribopicker/0.4.3 module load gcc/4.8.2 gdc perl/5.18.4 ribopicker/0.4.3
rmblast/2.2.28 module load gcc/4.8.2 gdc rmblast/2.2.28
rmblast/2.6.0 module load gcc/4.8.2 gdc rmblast/2.6.0
rsem/1.3.3 module load gcc/4.8.2 gdc bowtie/1.1.2 bowtie2/2.3.4.2 star/2.7.0a hisat2/2.1.0 perl/5.18.4 bioconductor/3.4 python/3.6.1 rsem/1.3.3
rtg-tools/3.8.4 module load gcc/4.8.2 gdc java/1.8.0_101 rtg-tools/3.8.4
salmon/0.13.1 module load new gcc/5.2.0 gdc boost/1.62.0 salmon/0.13.1
salmon/0.14.1 module load new gcc/5.2.0 gdc boost/1.62.0 salmon/0.14.1
salmon/0.9.1 module load gcc/4.8.2 gdc boost/1.55.0 salmon/0.9.1
salmonte/0.3 module load gcc/4.8.2 gdc python/3.6.1 openblas/0.2.13_seq bzip2/1.0.6 zlib/1.2.8 xz/5.2.2 pcre/8.38 curl/7.51 bioconductor/3.4 salmonte/0.3
salsa/1.0 module load gcc/4.8.2 gdc perl/5.18.4 python/2.7.11 samtools/1.3 bedtools/2.25 salsa/1.0
salsa/2.0 module load gcc/4.8.2 gdc perl/5.18.4 python/2.7.11 samtools/1.3 bedtools/2.25 boost/1.63.0 salsa/2.0
sambamba/0.6.1 module load gcc/4.8.2 gdc sambamba/0.6.1
sambamba/0.6.6 module load gcc/4.8.2 gdc sambamba/0.6.6
sambamba/0.6.8 module load gcc/4.8.2 gdc sambamba/0.6.8
sambamba/0.7.1 module load gcc/4.8.2 gdc sambamba/0.7.1
sambamba/0.8.0 module load gcc/4.8.2 gdc sambamba/0.8.0
samblaster/0.1.22 module load gcc/4.8.2 gdc samblaster/0.1.22
samtools/1.10 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.10
samtools/1.3 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.3
samtools/1.7 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.7
samtools/1.8 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.8
samtools/1.9 module load gcc/4.8.2 gdc perl/5.18.4 samtools/1.9
segemehl/0.2.0 module load gcc/4.8.2 gdc segemehl/0.2.0
se-mei/1.0 module load gcc/4.8.2 gdc python/2.7.11 se-mei/1.0
seqkit/0.7.2 module load gcc/4.8.2 gdc seqkit/0.7.2
seqprep/1 module load gcc/4.8.2 gdc seqprep/1
seqtk/1.2-r94 module load gcc/4.8.2 gdc seqtk/1.2-r94
sga/0.10.14 module load gcc/4.8.2 gdc python/2.7.11 perl/5.18.4 bamtools/2.4.0 sga/0.10.14
shapeit/26082019 module load new gcc/5.2.0 gdc samtools/1.7 boost/1.62.0 shapeit/26082019
shapeit/4.1.2 module load new gcc/5.2.0 gdc samtools/1.7 boost/1.62.0 shapeit/4.1.2
shore/0.9.3 module load gcc/4.8.2 gdc boost/1.55.0 gsl/1.16 zlib/1.2.8 xz/5.2.2 genomemapper/0.4.4 shore/0.9.3
smrt_analysis/2.3.0_p5 module load gcc/4.8.2 gdc smrt_analysis/2.3.0_p5
smrt_link/5.0.1.9585 module load gcc/4.8.2 gdc smrt_link/5.0.1.9585
snap/2006-07-28 module load gcc/4.8.2 gdc perl/5.18.4 snap/2006-07-28
snippy/4.0-dev2 module load gcc/4.8.2 gdc perl/5.18.4 bzip2/1.0.6 java/1.8.0_101 snippy/4.0-dev2
snippy/4.4.5 module load gcc/4.8.2 gdc perl/5.18.4 bzip2/1.0.6 java/1.8.0_101 snippy/4.4.5
snpeff/4.3m module load gcc/4.8.2 gdc java/1.8.0_73 snpeff/4.3m
snpgenie/1.0 module load gcc/4.8.2 gdc perl/5.18.4 snpgenie/1.0
soapdenovo2/2.04 module load gcc/4.8.2 gdc soapdenovo2/2.04
sonics/0.1.0 module load gcc/4.8.2 gdc python/3.6.1 sonics/0.1.0
sortmerna/2.1 module load gcc/4.8.2 gdc sortmerna/2.1
spades/3.10.0 module load gcc/4.8.2 gdc python/2.7.11 spades/3.10.0
spades/3.11.1 module load gcc/4.8.2 gdc python/2.7.11 spades/3.11.1
spades/3.14.0 module load new gcc/6.3.0 gdc python/2.7.11 spades/3.14.0
spades/3.14.1 module load new gcc/6.3.0 gdc python/2.7.11 spades/3.14.1
spades/3.6.2 module load gcc/4.8.2 gdc python/2.7.11 spades/3.6.2
spaunge/1.0 module load gcc/4.8.2 gdc spaunge/1.0
sqlite3/3.11 module load gcc/4.8.2 gdc sqlite3/3.11
sra-tools/2.10.8 module load new gcc/5.2.0 gdc sra-tools/2.10.8
sra-tools/2.7.0 module load gcc/4.8.2 gdc sra-tools/2.7.0
sra-tools/2.8.1-3 module load gcc/4.8.2 gdc sra-tools/2.8.1-3
stacks/1.37 module load gcc/4.8.2 gdc perl/5.18.4 stacks/1.37
stacks/1.40 module load gcc/4.8.2 gdc perl/5.18.4 stacks/1.40
stacks/2.0b module load gcc/4.9.2 gdc perl/5.18.4 stacks/2.0b
stacks/2.41 module load gcc/4.9.2 gdc perl/5.18.4 stacks/2.41
stampy/1.0.22 module load gcc/4.8.2 gdc python/2.7.11 stampy/1.0.22
star/2.7.0a module load gcc/4.8.2 gdc star/2.7.0a
stringtie/1.3.3b module load gcc/4.8.2 gdc stringtie/1.3.3b
structure/2.3.4 module load gcc/4.8.2 gdc structure/2.3.4
suitesparse/4.5.1 module load gcc/4.8.2 gdc openblas/0.2.13_seq suitesparse/4.5.1
supernova/2.1.1 module load gcc/4.8.2 gdc supernova/2.1.1
swig/3.0.8 module load gcc/4.8.2 gdc python/3.4.3 swig/3.0.8
tadbit/0.2 module load gcc/4.8.2 gdc hdf5/1.8.12 open_mpi/1.6.5 boost/1.63.0 python/2.7.11 tadbit/0.2
tlex/2.2.1 module load gcc/4.8.2 gdc perl/5.18.4 blat/35 hmmer/3.1 rmblast/2.2.28 repeatmasker/4.0.6 tlex/2.2.1
tophat/1.4.1 module load gcc/4.8.2 gdc python/2.7.11 tophat/1.4.1
tophat/2.1.1 module load gcc/4.8.2 gdc boost/1.55.0 python/2.7.11 tophat/2.1.1
transdecoder/3.0.1 module load gcc/4.8.2 gdc perl/5.18.4 transdecoder/3.0.1
transdecoder/5.3.0 module load gcc/4.8.2 gdc perl/5.18.4 transdecoder/5.3.0
trim_galore/0.4.5 module load gcc/4.8.2 gdc perl/5.18.4 python/2.7.11 java/1.8.0_73 fastqc/0.11.4 trim_galore/0.4.5
trimmomatic/0.35 module load gcc/4.8.2 gdc java/1.8.0_73 trimmomatic/0.35
trinity/2.1.1 module load gcc/4.8.2 gdc bowtie/1.1.2 python/2.7.11 perl/5.18.4 java/1.8.0_73 trinity/2.1.1
trinity/2.11.0 module load new gcc/5.2.0 gdc bowtie2/2.3.2 python/3.6.1 perl/5.18.4 java/1.8.0_101 samtools/1.9 jellyfish/2.2.10 boost/1.62.0 salmon/0.14.1 trinity/2.11.0
trinity/2.4.0 module load gcc/4.8.2 gdc bowtie2/2.2.6 python/2.7.11 perl/5.18.4 java/1.8.0_73 trinity/2.4.0
trinity/2.5.1 module load gcc/4.8.2 gdc bowtie2/2.2.6 python/2.7.11 perl/5.18.4 java/1.8.0_101 trinity/2.5.1
trinity/2.8.4 module load new gcc/5.2.0 gdc bowtie2/2.3.2 python/2.7.11 perl/5.18.4 java/1.8.0_101 samtools/1.9 jellyfish/2.2.10 boost/1.62.0 salmon/0.14.1 trinity/2.8.4
tulip/0.4 module load gcc/4.8.2 gdc perl/5.18.4 tulip/0.4
twisst/1.0 module load gcc/4.8.2 gdc python/2.7.11 twisst/1.0
usearch/11.0.667 module load gcc/4.8.2 gdc usearch/11.0.667
usearch/8.1 module load gcc/4.8.2 gdc usearch/8.1
vcflib/1.0.0 module load gcc/4.8.2 gdc vcflib/1.0.0
vcflib/1.0.1 module load gcc/4.8.2 gdc vcflib/1.0.1
vcflib/1.0.1.1 module load gcc/4.8.2 gdc vcflib/1.0.1.1
vcftools/0.1.14 module load gcc/4.8.2 gdc perl/5.18.4 vcftools/0.1.14
vcftools/0.1.15 module load gcc/4.8.2 gdc perl/5.18.4 zlib/1.2.8 vcftools/0.1.15
vcftools/0.1.16 module load gcc/4.8.2 gdc perl/5.18.4 zlib/1.2.8 vcftools/0.1.16
velvet/1.2.10 module load gcc/4.8.2 gdc velvet/1.2.10
vsearch/2.15.1 module load gcc/4.8.2 gdc vsearch/2.15.1
vt/0.5 module load gcc/4.8.2 gdc vt/0.5
xz/5.2.2 module load gcc/4.8.2 gdc xz/5.2.2
yaha/0.1.83 module load gcc/4.8.2 gdc yaha/0.1.83
zlib/1.2.8 module load gcc/4.8.2 gdc zlib/1.2.8


Available tools and libraries (new software stack)

This is work in progress. We will provide soon the list of bioinformatics tools available in the new software stack, including the module commands. The new software stack features the concept of toolchains and a module hierarchy using LMOD modules. A toolchain is a combination of a compiler and eventually an MPI library. Packages are then compiled for one or more toolchains. Due to the module hierarchy, you can only load one compiler at the time and you can only load packages that are available for the compiler module you have loaded (with the exceptions of Core modules, which can be loaded for all available compilers). This is to prevent conflicts that users can encounter when mixing tools that were compiled with different compiler versions. A full overview on all available modules (not just bioinformatics) is provided as well on our wiki.

The list provides the information for which toolchain (GCC 4.8.5, 6.3.0, 8.2.0 and Intel 19.1.0) a software is available and how the module command looks like. Please note that you need to have the corresponding GCC version loaded to be able to load the module of the bioinformatics tool. For instance, the freebayes 1.3.5 module is available for the GCC 6.3.0 and 8.2.0 toolchain but not for GCC 4.8.5. You can load the module in the GCC 6.3.0 toolchain with the command

module load gcc/6.3.0 freebayes/1.3.5

and for the GCC 8.2.0 toolchain with the command

module load gcc/8.2.0 freebayes/1.3.5

Please note that if you already have the corresponding gcc module loaded, then you don't need to load it again and can directly load the freebayes module.

Application GCC 4.8.5 GCC 6.3.0 GCC 8.2.0 Intel 19.1.0 Module load command
angsd 0.921 module load angsd/0.921
angsd 0.925 module load angsd/0.925
armadillo 9.700.2 module load openmpi/4.0.2 armadillo/9.700.2
augustus 3.4.0 module load augustus/3.4.0
bamtools 2.5.1 module load bamtools/2.5.1
bamutil 1.0.13 module load bamutil/1.0.13
bbmap 37.36 module load bbmap/37.36
bcl2fastq 2.20.422 module load bcl2fastq/2.20.422
beagle 3.3.2 module load beagle/3.3.2
beagle 4.1 module load beagle/4.1
beagle 5.1 module load beagle/5.1
bedops 2.4.36 module load bedops/2.4.36
bedtools2 2.26.0 module load bedtools2/2.26.0
bedtools2 2.27.1 module load bedtools2/2.27.1
bedtools2 2.29.2 module load bedtools2/2.29.2
bedtools2 2.30.0 module load bedtools2/2.30.0
bismark 0.19.0 module load bismark/0.19.0
blast+ 2.9.0 module load blast-plus/2.9.0
blat 35 module load blat/35
blat 36 module load blat/36
bowtie 1.2 module load bowtie/1.2
bowtie 1.3.0 module load bowtie/1.3.0
bowtie2 2.3.4.1 module load bowtie2/2.3.4.1
bowtie2 2.3.5.1 module load bowtie2/2.3.5.1
bowtie2 2.4.4 module load bowtie2/2.4.4
breseq 0.30.1 module load breseq/0.30.1
breseq 0.32.0 module load breseq/0.32.0
breseq 0.34.1 module load breseq/0.34.1
breseq 0.36.0 module load breseq/0.36.0
bwa 0.7.12 module load bwa/0.7.12
bwa 0.7.15 module load bwa/0.7.15
bwa 0.7.17 module load bwa/0.7.17
canu 1.9 module load canu/1.9
cd-hit 4.6.8 module load cdhit/4.6.8
clustalo 1.2.4 module load clustalo/1.2.4
clustalw 2.1 module load clustalw/2.1
diamond 0.9.14 module load diamond/0.9.14
diamond 0.9.22 module load diamond/0.9.22
diamond 0.9.24 module load diamond/0.9.24
diamond 0.9.28 module load diamond/0.9.28
diamond 2.0.6 module load diamond/2.0.6
emboss 6.6.0 module load emboss/6.6.0
exonerate 2.4.0 module load exonerate/2.4.0
fastani 1.33 module load fastani/1.33
fastqc 0.11.4 module load fastqc/0.11.4
fastqc 0.11.5 module load fastqc/0.11.5
fastqc 0.11.9 module load fastqc/0.11.9
fastqscreen 0.11.2 module load fastq-screen/0.11.2
fasttree 2.1.11 module load fasttree/2.1.11
fastx_toolkit 0.0.14 module load fastx-toolkit/0.0.14
flash 1.2.11 module load flash/1.2.11
freebayes 1.3.5 module load freebayes/1.3.5
gatk 4.0.4.0 module load gatk/4.0.4.0
gatk 4.0.10.0 module load gatk/4.0.10.0
gatk 4.1.1.0 module load gatk/4.1.1.0
gatk 4.2.1.0 module load gatk/4.2.1.0
gemma 0.98.5 module load gemma/0.98.5
guppy (CPU) 5.0.16 module load guppy-cpu/5.0.16
hisat2 2.1.0 module load hisat2/2.1.0
hisat2 2.2.1 module load hisat2/2.2.1
hmmer 3.1 b2 module load openmpi/4.0.2 hmmer/3.1b2
htslib 1.2 module load htslib/1.2
htslib 1.3.1 module load htslib/1.3.1
htslib 1.6 module load htslib/1.6
htslib 1.7 module load htslib/1.7
htslib 1.10.2 module load htslib/1.10.2
htslib 1.12 module load htslib/1.12
idba 1.1.3 module load idba/1.1.3
itsx 1.1.3 module load openmpi/4.0.2 itsx/1.1.3
mafft 7.221 module load mafft/7.221
mash 2.3 module load mash/2.3
mcl 14.137 module load mcl/14-137
megahit 1.1.4 module load megahit/1.1.4
minimap2 2.17 module load minimap2/2.17
motus 3.1 module load motus/3.1
muscle 3.8.31 module load muscle/3.8.31
muscle 3.8.1551 module load muscle/3.8.1551
picard 2.18.14 module load picard/2.18.14
picard 2.23.2 module load picard/2.23.2
picard 2.25.7 module load picard/2.25.7
plink 1.9 beta6.18 module load plink/1.9-beta6.18
pplacer 1.1 alpha19 module load pplacer/1.1.alpha19
primer3 2.4.0 module load primer3/2.4.0
prinseq-lite 0.20.4 module load prinseq-lite/0.20.4
prodigal 2.6.3 module load prodigal/2.6.3
raxml 2.8.12 module load openmpi/4.0.2 raxml/2.8.12
sambamba 0.8.1 module load sambamba/0.8.1
samtools 1.2 module load samtools/1.2
samtools 1.6 module load samtools/1.6
samtools 1.10 module load samtools/1.10
samtools 1.12 module load samtools/1.12
seqkit 0.16.1 module load seqkit/0.16.1
seqtk 1.2 module load seqtk/1.2
seqtk 1.3 module load seqtk/1.3
spades 3.6.2 module load spades/3.6.2
spades 3.10.0 module load spades/3.10.0
spades 3.11.1 module load spades/3.11.1
spades 3.14.0 module load spades/3.14.0
sra toolkit 2.8.1 module load sra-toolkit/2.8.1
sra toolkit 2.8.2-1 module load sra-toolkit/2.8.2-1
sra toolkit 2.9.2 module load sra-toolkit/2.9.2
sra toolkit 2.10.5 module load sra-toolkit/2.10.5
stacks 2.59 module load stacks/2.59
star 2.5.3 a module load star/2.5.3a
star 2.7.2 d module load star/2.7.2d
star 2.7.9 a module load star/2.7.9a
tophat 2.1.2 module load tophat/2.1.2
trimmomatic 0.35 module load trimmomatic/0.35
trimmomatic 0.36 module load trimmomatic/0.36
trimmomatic 0.38 module load trimmomatic/0.38
usearch 11.0.667 module load usearch/11.0.667
vcftools 0.1.14 module load vcftools/0.1.14
velvet 1.2.10 module load velvet/1.2.10
vsearch 2.14.1 module load vsearch/2.14.1