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list-of-software [2019/03/12 09:48]
jean-baka
list-of-software [2020/08/09 13:05] (current)
aorth
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 |[[artemis-software|artemis]]|16.0.0|''module load act/16.0.0''| | |[[artemis-software|artemis]]|16.0.0|''module load act/16.0.0''| |
 |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| | |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| |
 +|[[awscli-software|awscli]]|1.17.9|''module load awscli/1.17.9''| |
 |[[bam-readcount-software|bam-readcount]]|0.8.0|''module load bam-readcount/0.8.0''| | |[[bam-readcount-software|bam-readcount]]|0.8.0|''module load bam-readcount/0.8.0''| |
 |[[bamtools-software|bamtools]]|2.5.1|''module load bamtools/2.5.1''| | |[[bamtools-software|bamtools]]|2.5.1|''module load bamtools/2.5.1''| |
 +|[[barrnap-software|barrnap]]|0.9|''module load barrnap/0.9''| |
 |bayescan|2.1|''module load bayescan/2.1''| | |bayescan|2.1|''module load bayescan/2.1''| |
 +|[[bbmap-software|bbmap]]|38.67|''module load bbmap/38.67''| |
 |[[bcftools-software|bcftools]]|1.8|''module load bcftools/1.8''| | |[[bcftools-software|bcftools]]|1.8|''module load bcftools/1.8''| |
-|[[beagle-software|beagle]]|3.0.2|''module load beagle/3.0.2''| | +|[[beagle-software|beagle]]|3.1.2|''module load beagle/3.1.2''| | 
-|[[beast-software|beast]]|1.10.2|''module load beast/1.10.2''| |+|[[beast-software|beast]]|1.10.4|''module load beast/1.10.4''| |
 |[[bedops-software|bedops]]|2.4.29|''module load bedops/2.4.29''| | |[[bedops-software|bedops]]|2.4.29|''module load bedops/2.4.29''| |
-|[[bedtools-software|bedtools]]|2.25.0|''module load bedtools/2.25.0''| |+|[[bedtools-software|bedtools]]|2.29.0|''module load bedtools/2.29.0''| |
 |[[binpacker-software|binpacker]]|1.0|''module load binpacker/1.0''| | |[[binpacker-software|binpacker]]|1.0|''module load binpacker/1.0''| |
 |[[bioperl-software|bioperl]]|1.7.2|''module load bioperl/1.7.2''| | |[[bioperl-software|bioperl]]|1.7.2|''module load bioperl/1.7.2''| |
 |[[bitseq-software|bitseq]]|0.7.5|''module load bitseq/0.7.5''| | |[[bitseq-software|bitseq]]|0.7.5|''module load bitseq/0.7.5''| |
 |[[blasr-software|blasr]]|smrtanalysis-4.0.0|''module load blasr/smrtanalysis-4.0.0''| | |[[blasr-software|blasr]]|smrtanalysis-4.0.0|''module load blasr/smrtanalysis-4.0.0''| |
-|[[blast-software|blast]]|2.6.0+|''module load blast/2.6.0+''| |+|[[blast-software|blast]]|2.10.0+|''module load blast/2.10.0+''| |
 |[[blobtools-software|blobtools]]|0.9.19.3|''module load blobtools/0.9.19.3''| | |[[blobtools-software|blobtools]]|0.9.19.3|''module load blobtools/0.9.19.3''| |
 |blat|06-Aug-2013|''module load blat/06-Aug-2013''| | |blat|06-Aug-2013|''module load blat/06-Aug-2013''| |
-|[[bowtie-software|bowtie1 ]]|1.1.1|''module load bowtie/1.1.1''| |+|[[bowtie-software|bowtie1 ]]|1.2.3|''module load bowtie/1.2.3''| |
 |[[bowtie2-software|bowtie2 ]]|2.3.4.1|''module load bowtie2/2.3.4.1''| | |[[bowtie2-software|bowtie2 ]]|2.3.4.1|''module load bowtie2/2.3.4.1''| |
 |[[brig-software|brig]]|0.95|''module load brig/0.95''| | |[[brig-software|brig]]|0.95|''module load brig/0.95''| |
-|[[busco-software|BUSCO ]]|3.0.2|''module load BUSCO/3.0.2''| | +|[[busco-software|BUSCO ]]|4.0.6|''module load BUSCO/4.0.6''| | 
-|[[bwa-software|bwa]]|0.7.15|''module load bwa/0.7.15''| |+|[[bwa-software|bwa]]|0.7.17|''module load bwa/0.7.17''| |
 |[[cafe-software|cafe]]|4.1|''module load cafe/4.1''| | |[[cafe-software|cafe]]|4.1|''module load cafe/4.1''| |
 |cangs|1.1|''module load cangs/1.1''| | |cangs|1.1|''module load cangs/1.1''| |
Line 50: Line 53:
 |celera-wgs|6.1|''module load celera-wgs/6.1''| | |celera-wgs|6.1|''module load celera-wgs/6.1''| |
 |censor|4.2.28|''module load censor/4.2.28''| | |censor|4.2.28|''module load censor/4.2.28''| |
-|[[changeo-software|changeo]]|0.3.9|''module load changeo/0.3.9''| | +|[[changeo-software|changeo]]|1.0.0|''module load changeo/1.0.0''| | 
-|[[circos-software|circos]]|0.67|''module load circos/0.67''| |+|[[checkm-software|checkm]]|1.1.2|''module load checkm/1.1.2''| | 
 +|[[circos-software|circos]]|0.69-9|''module load circos/0.69-9''| |
 |[[clonalframe-software|clonalframe]]|1.2|''module load clonalframe/1.2''| | |[[clonalframe-software|clonalframe]]|1.2|''module load clonalframe/1.2''| |
 |[[clonalframeml-software|clonalframeml]]|1.0|''module load clonalframeml/1.0''| | |[[clonalframeml-software|clonalframeml]]|1.0|''module load clonalframeml/1.0''| |
Line 65: Line 69:
 |dendroscope|2.7.4|''module load dendroscope/2.7.4''| | |dendroscope|2.7.4|''module load dendroscope/2.7.4''| |
 |[[diamond-software|diamond]]|0.9.9|''module load diamond/0.9.9''| | |[[diamond-software|diamond]]|0.9.9|''module load diamond/0.9.9''| |
 +|[[drep-software|drep]]|2.5.4|''module load drep/2.5.4''| |
 |[[ea-utils-software|ea-utils]]|1.04.807|''module load ea-utils/1.04.807''| | |[[ea-utils-software|ea-utils]]|1.04.807|''module load ea-utils/1.04.807''| |
 |[[edirect-software|edirect]]| 7.80 | ''module load edirect/7.80'' | | |[[edirect-software|edirect]]| 7.80 | ''module load edirect/7.80'' | |
Line 73: Line 78:
 |[[exabayes-software|exabayes]]|1.4.1|''module load exabayes/1.4.1''| | |[[exabayes-software|exabayes]]|1.4.1|''module load exabayes/1.4.1''| |
 |[[express-software|express]]|1.5.1|''module load express/1.5.1''| | |[[express-software|express]]|1.5.1|''module load express/1.5.1''| |
 +|[[fastANI-software|fastANI]]|1.3|''module load fastANI/1.3''| |
 |[[fastPHASE-software|fastPHASE]]|1.4.8|''module load fastPHASE/1.4.8''| | |[[fastPHASE-software|fastPHASE]]|1.4.8|''module load fastPHASE/1.4.8''| |
 |[[fastqc-software|fastqc]]|0.11.7|''module load fastqc/0.11.7''| | |[[fastqc-software|fastqc]]|0.11.7|''module load fastqc/0.11.7''| |
 |[[faststructure-software|fastSTRUCTURE]]|1.0|''module load fastSTRUCTURE/1.0''| | |[[faststructure-software|fastSTRUCTURE]]|1.0|''module load fastSTRUCTURE/1.0''| |
 +|[[fasttree-software|fasttree]]|2.1.11|''module load fasttree/2.1.11''| |
 |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|''module load fastx_toolkit/0.0.13''| | |[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|''module load fastx_toolkit/0.0.13''| |
 |figtree|1.4.0|''module load figtree/1.4.0''| | |figtree|1.4.0|''module load figtree/1.4.0''| |
Line 83: Line 90:
 |[[flexbar-software|flexbar]]|2.7.0|''module load flexbar/2.7.8''| | |[[flexbar-software|flexbar]]|2.7.0|''module load flexbar/2.7.8''| |
 |[[flux-capacitor-software|flux-capacitor]]|1.6.1|''module load flux-capacitor/1.6.1''| | |[[flux-capacitor-software|flux-capacitor]]|1.6.1|''module load flux-capacitor/1.6.1''| |
 +|[[flye-software|flye]]|2.4.2|''module load flye/2.4.2''| |
 |frappe|1.1|''module load frappe/1.1''| | |frappe|1.1|''module load frappe/1.1''| |
-|[[fraggenescan-software|FragGeneScan ]]|1.19|''module load fraggenescan/1.19''| |+|[[fraggenescan-software|FragGeneScan ]]|1.30|''module load fraggenescan/1.30''| |
 |[[freebayes-software|FreeBayes ]]|1.0.2|''module load freebayes/1.0.2''| | |[[freebayes-software|FreeBayes ]]|1.0.2|''module load freebayes/1.0.2''| |
 |[[gassflow-software|GassFlow ]]|1.0|''module load gassflow/1.0''| | |[[gassflow-software|GassFlow ]]|1.0|''module load gassflow/1.0''| |
Line 100: Line 108:
 |[[groovy-software|groovy]]|2.4.9|''module load groovy/2.4.9''| | |[[groovy-software|groovy]]|2.4.9|''module load groovy/2.4.9''| |
 |[[gsea-software|GSEA]]|2.2.3|''module load gsea/2.2.3''| | |[[gsea-software|GSEA]]|2.2.3|''module load gsea/2.2.3''| |
 +|[[gtdbtk-software|gtdbtk]]|1.1.1|''module load gtdbtk/1.1.1''| |
 |[[guidance-software|guidance]]|2.02|''module load guidance/2.02''| | |[[guidance-software|guidance]]|2.02|''module load guidance/2.02''| |
 |[[hapflk-software|hapflk]]|1.4|''module load hapflk/1.4''| | |[[hapflk-software|hapflk]]|1.4|''module load hapflk/1.4''| |
 |hapmix|2.0|''module load hapmix/2.0''| | |hapmix|2.0|''module load hapmix/2.0''| |
 |[[hdf5-software|hdf5]]|1.8.19|''module load hdf5/1.8.19''| | |[[hdf5-software|hdf5]]|1.8.19|''module load hdf5/1.8.19''| |
-|[[hmmer-software|hmmer]]|3.1b2|''module load hmmer/3.1b2''| |+|[[hmmer-software|hmmer]]|3.3|''module load hmmer/3.3''| |
 |[[hpg-variant-software|hpg-variant]]|1.0|''module load hpg-variant/1.0''| | |[[hpg-variant-software|hpg-variant]]|1.0|''module load hpg-variant/1.0''| |
 |[[hisat2-software|hisat2]]|2.1.0|''module load hisat2/2.1.0''| | |[[hisat2-software|hisat2]]|2.1.0|''module load hisat2/2.1.0''| |
-|[[htseq-software|htseq]]|0.6.1|''module load htseq/0.6.1''| | +|[[htseq-software|htseq]]|0.9.1|''module load htseq/0.9.1''| | 
-|[[htslib-software|htslib]]|1.8|''module load htslib/1.8''| | +|[[htslib-software|htslib]]|1.9|''module load htslib/1.9''| | 
-|[[igblast-software|igblast]]|1.6.0|''module load igblast/1.6.0''| |+|[[idba-software|idba]]|1.1.2|''module load idba/1.1.2''| | 
 +|[[igblast-software|igblast]]|1.10.0|''module load igblast/1.10.0''| | 
 +|[[igdiscover-software|igdiscover]]|0.12.3|''module load igdiscover/0.12.3''| |
 |[[igrec-software|igrec]]|3.0.0|''module load igrec/3.0.0''| | |[[igrec-software|igrec]]|3.0.0|''module load igrec/3.0.0''| |
 +|[[igsimulator-software|igsimulator]]|git-c3778b74|''module load igsimulator/git-c3778b74''| |
 +|[[igtree-software|iqtree]]|1.6.12|''module load iqtree/1.6.12''| |
 |[[igv-software|igv]]|2.4.5|''module load igv/2.4.5''| | |[[igv-software|igv]]|2.4.5|''module load igv/2.4.5''| |
 |[[igvtools-software|igvtools]]|2.3.98|''module load igvtools/2.3.98''| | |[[igvtools-software|igvtools]]|2.3.98|''module load igvtools/2.3.98''| |
 +|[[infernal-software|infernal]]|1.1.2|''module load infernal/1.1.2''| |
 |[[interproscan-software|interproscan]]|5.13|''module load interproscan/5.13''| | |[[interproscan-software|interproscan]]|5.13|''module load interproscan/5.13''| |
 |i-tasser|latest|''module load i-tasser/latest''| | |i-tasser|latest|''module load i-tasser/latest''| |
Line 125: Line 139:
 |[[kmergenie-software|kmergenie]]|1.7038|''module load kmergenie/1.7038''| | |[[kmergenie-software|kmergenie]]|1.7038|''module load kmergenie/1.7038''| |
 |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|''module load kmer-ssr/git-4043c0e7''| | |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|''module load kmer-ssr/git-4043c0e7''| |
-|[[kraken-software|kraken]]|0.10.5|''module load kraken/0.10.5''| |+|[[kraken-software|kraken]]|2.0.8-beta|''module load kraken/2.0.8-beta''| |
 |krona|2.4|''module load krona/2.4''| | |krona|2.4|''module load krona/2.4''| |
 |lamp|2.5|''module load lamp/2.5''| | |lamp|2.5|''module load lamp/2.5''| |
Line 132: Line 146:
 |[[libsvm-software|libsvm]]|3.20|''module load libsvm/3.20''| | |[[libsvm-software|libsvm]]|3.20|''module load libsvm/3.20''| |
 |[[lighter-software|lighter]]|1.1.2|''module load lighter/1.1.2''| | |[[lighter-software|lighter]]|1.1.2|''module load lighter/1.1.2''| |
 +|[[lordec-software|lordec]]|0.9|''module load lordec/0.9''| |
 |lucy|1.19p|''module load lucy/1.19p''| | |lucy|1.19p|''module load lucy/1.19p''| |
 |[[mafft-software|mafft]]|7.313|''module load mafft/7.313''| | |[[mafft-software|mafft]]|7.313|''module load mafft/7.313''| |
 |[[mapsplice-software|mapsplice]]|2.2.0|''module load mapsplice/2.2.0''| | |[[mapsplice-software|mapsplice]]|2.2.0|''module load mapsplice/2.2.0''| |
 |[[marginalign-software|marginalign]]|git-2369dafd|''module load marginalign/git-2369dafd''| | |[[marginalign-software|marginalign]]|git-2369dafd|''module load marginalign/git-2369dafd''| |
-|[[mash-software|mash]]|2.0|''module load mash/2.0''| | +|[[marginpolish-software|marginpolish]]|1.0.0|''module load marginpolish/1.0.0''| | 
-|[[masurca-software|masurca]]|3.2.8|''module load masurca/3.2.8''| |+|[[mash-software|mash]]|2.2|''module load mash/2.2''| | 
 +|[[masurca-software|masurca]]|3.3.1|''module load masurca/3.3.1''| |
 |mauve|2.3.1|''module load mauve/2.3.1''| | |mauve|2.3.1|''module load mauve/2.3.1''| |
 +|[[maxbin2-software|maxbin2]]|2.2.7|''module load maxbin2/2.2.7''| |
 |maximus|0.2|''module load maximus/0.2''| | |maximus|0.2|''module load maximus/0.2''| |
 |[[mcl-software|mcl]]|14-137|''module load mcl/14-137''| | |[[mcl-software|mcl]]|14-137|''module load mcl/14-137''| |
 |[[mecat-software|MECAT]]|git-d04bfa84|''module load MECAT/git-d04bfa84''| | |[[mecat-software|MECAT]]|git-d04bfa84|''module load MECAT/git-d04bfa84''| |
 +|[[medaka-software|medaka]]|0.8.2|''module load medaka/0.8.2''| |
 |[[megahit-software|megahit]]|1.1.4|''module load megahit/1.1.4''| | |[[megahit-software|megahit]]|1.1.4|''module load megahit/1.1.4''| |
 |megan|4.70.4|''module load megan/4.70.4''| | |megan|4.70.4|''module load megan/4.70.4''| |
 +|[[megax-software|megax]]|10.0.5|''module load megax/10.0.5''| |
 |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| | |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| |
 +|[[metaphlan2-software|metaphlan2]]|2.9.5|''module load metaphlan2/2.9.5''| |
 |[[metis-software|metis]]|5.1.0|''module load metis/5.1.0''| | |[[metis-software|metis]]|5.1.0|''module load metis/5.1.0''| |
 |[[migec-software|migec]]|1.2.4a|''module load migec/1.2.4a''| | |[[migec-software|migec]]|1.2.4a|''module load migec/1.2.4a''| |
Line 151: Line 171:
 |[[minimap2-software|minimap2]]|2.13|''module load minimap2/2.13''| | |[[minimap2-software|minimap2]]|2.13|''module load minimap2/2.13''| |
 |[[minpath-software|MinPath]]|1.0.2|''module load MinPath/1.2''| | |[[minpath-software|MinPath]]|1.0.2|''module load MinPath/1.2''| |
-|[[mira-software#v4.0.2|mira ]]|4.0.2|''module load mira/4.0.2''| |+|[[mira-software#v4.0.2|mira]]|4.0.2|''module load mira/4.0.2''| | 
 +|[[mirdeep2-software|mirdeep2]]|0.1.3|''module load mirdeep2/0.1.3''| |
 |[[mitools-software|mitools]]|1.4|''module load mitools/1.4''| | |[[mitools-software|mitools]]|1.4|''module load mitools/1.4''| |
-|[[mixcr-software|mixcr]]|2.0.1|''module load mixcr/2.0.1''| |+|[[mixcr-software|mixcr]]|3.0.11|''module load mixcr/3.0.11''| |
 |mkatari-ilri|latest|''module load mkatari-ilri/latest''| | |mkatari-ilri|latest|''module load mkatari-ilri/latest''| |
 |[[modeller-software|modeller]]|9.17|''module load modeller/9.17''| | |[[modeller-software|modeller]]|9.17|''module load modeller/9.17''| |
-|[[mothur-software|mothur]]|1.39.5|''module load mothur/1.39.5''| |+|[[mothur-software|mothur]]|1.44.1|''module load mothur/1.44.1''| |
 |[[mothur-krona-software|mothur-krona]]|git-87499a0|''module load mothur-krona/git-87499a0''| | |[[mothur-krona-software|mothur-krona]]|git-87499a0|''module load mothur-krona/git-87499a0''| |
 |mpiblast|1.6.0|''module load mpiblast/1.6.0''| | |mpiblast|1.6.0|''module load mpiblast/1.6.0''| |
 |mrbayes|3.2.2|''module load mrbayes/3.2.2''| | |mrbayes|3.2.2|''module load mrbayes/3.2.2''| |
 |[[multiqc-software|multiqc]]|1.4|''module load multiqc/1.4''| | |[[multiqc-software|multiqc]]|1.4|''module load multiqc/1.4''| |
-|[[muscle-software|muscle]]|3.8.31|''module load muscle/3.8.31'' |+|[[muscle-software|muscle]]|3.8.1551|''module load muscle/3.8.1551'' |
 |[[mummer-software|MUMmer]]|3.23|''module load MUMmer/3.23''| | |[[mummer-software|MUMmer]]|3.23|''module load MUMmer/3.23''| |
 |[[nanopolish-software|nanopolish]]|0.10.2|''module load nanopolish/0.10.2''| | |[[nanopolish-software|nanopolish]]|0.10.2|''module load nanopolish/0.10.2''| |
 |[[netmhcpan-software|netmhcpan]]|2.8|''module load netmhcpan/2.8''| | |[[netmhcpan-software|netmhcpan]]|2.8|''module load netmhcpan/2.8''| |
 |[[nextclip-software|nextclip]]|1.3.1|''module load nextclip/1.3.1''| | |[[nextclip-software|nextclip]]|1.3.1|''module load nextclip/1.3.1''| |
 +|[[nextflow-software|nextflow]]|20.04.1|''module load nextflow/20.04.1''| |
 |[[ntcard-software|ntCard]]|1.0.0|''module load ntCard/1.0.0''| | |[[ntcard-software|ntCard]]|1.0.0|''module load ntCard/1.0.0''| |
 |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|''module load ngsqctoolkit/2.3.3''| | |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|''module load ngsqctoolkit/2.3.3''| |
 |novacraft|3.02.07|''module load novacraft/3.02.07''| | |novacraft|3.02.07|''module load novacraft/3.02.07''| |
 |[[oases-software|oases]]|0.2.08|''module load oases/0.2.08''| | |[[oases-software|oases]]|0.2.08|''module load oases/0.2.08''| |
-|[[ocaml-software#v4.02.1|ocaml ]]|4.02.1|''module load ocaml/4.02.1''| | +|[[ocaml-software#v4.02.1|ocaml]]|4.02.1|''module load ocaml/4.02.1''| | 
-|[[opam-software#v1.2.0|opam ]]|1.2.0|''module load opam/1.2.0''| |+|[[opam-software#v1.2.0|opam]]|1.2.0|''module load opam/1.2.0''| |
 |orthomcl|2.0.3|''module load orthomcl/2.0.3''| | |orthomcl|2.0.3|''module load orthomcl/2.0.3''| |
 +|[[orp-software|Oyster River Protocol]]|2.2.8|''module load orp/2.2.8''| |
 |[[pagan-software|pagan]]|0.61|''module load pagan/0.61''| | |[[pagan-software|pagan]]|0.61|''module load pagan/0.61''| |
 |[[pairfq-software|pairfq]]|0.14.4|''module load pairfq/0.14.4''| | |[[pairfq-software|pairfq]]|0.14.4|''module load pairfq/0.14.4''| |
Line 178: Line 201:
 |[[pandaseq-software|pandaseq]]|2.8.1|''module load pandaseq/2.8.1'' | |[[pandaseq-software|pandaseq]]|2.8.1|''module load pandaseq/2.8.1'' |
 |[[pasta-software|pasta]]|d939adb2|''module load pasta/d939adb2'' | |[[pasta-software|pasta]]|d939adb2|''module load pasta/d939adb2'' |
-|[[pear-software|pear]]|git-2c309dc|''module load pear/git-2c309dc''| |+|[[pear-software|pear]]|0.9.6|''module load pear/0.9.6''| | 
 +|[[pblat-software|pblat]]|2.1|''module load pblat/2.1''| |
 |[[pbsuite-software|pbsuite]]|15.8.24|''module load pbsuite/15.8.24''| | |[[pbsuite-software|pbsuite]]|15.8.24|''module load pbsuite/15.8.24''| |
-|[[perl-software|perl]]|5.22.3|''module load perl/5.22.3''| |+|[[perl-software|perl]]|5.28.2|''module load perl/5.28.2''| |
 |[[pgdspider-software|PGDSpider]]|2.1.1.0|''module load pgdspider/2.1.1.0''| | |[[pgdspider-software|PGDSpider]]|2.1.1.0|''module load pgdspider/2.1.1.0''| |
 |phrap|1.080812|''module load phrap/1.080812''| | |phrap|1.080812|''module load phrap/1.080812''| |
Line 190: Line 214:
 |[[pilon-software|pilon]]|1.23|''module load pilon/1.23''| | |[[pilon-software|pilon]]|1.23|''module load pilon/1.23''| |
 |[[platanus-software|platanus]]|1.2.1|''module load platanus/1.2.1''| | |[[platanus-software|platanus]]|1.2.1|''module load platanus/1.2.1''| |
-|[[plink-software|plink]]|1.9|''module load plink/1.9''| |+|[[plink-software|plink]]|2.00-alpha|''module load plink/2.00-alpha''| |
 |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| | |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| |
 +|[[porechop-software|porechop]]|0.2.4|''module load porechop/0.2.4''| |
 +|[[pplacer-software|pplacer]]|1.1.alpha19|''module load pplacer/1.1.alpha19''| |
 |[[prank-software|prank]]|170427|''module load prank/170427''| | |[[prank-software|prank]]|170427|''module load prank/170427''| |
-|[[presto-software|presto]]|0.5.3|''module load presto/0.5.3''| |+|[[presto-software|presto]]|0.5.13|''module load presto/0.5.13''| |
 |primer3|2.3.6|''module load primer3/2.3.6''| | |primer3|2.3.6|''module load primer3/2.3.6''| |
-|[[prokka-software|prokka]]|1.11|''module load prokka/1.11''| |+|[[prinseq-software|prinseq]]|0.20.4|''module load prinseq/0.20.4''| | 
 +|[[prodigal-software|prodigal]]|2.6.3|''module load prodigal/2.6.3''| | 
 +|[[prokka-software|prokka]]|1.14.6|''module load prokka/1.14.6''| |
 |[[provean-software|provean]]|1.1.5|''module load provean/1.1.5''| | |[[provean-software|provean]]|1.1.5|''module load provean/1.1.5''| |
-|[[python-software|python]]|3.7.2|''module load python/3.7''| |+|[[python-software|python]]|3.7.7|''module load python/3.7''| |
 |qdd|3_beta|''module load qdd/3_beta''| | |qdd|3_beta|''module load qdd/3_beta''| |
 |[[qiime-software|qiime]]|1.9.1|''module load qiime/1.9.1''| | |[[qiime-software|qiime]]|1.9.1|''module load qiime/1.9.1''| |
-|[[qiime2-software|qiime2]]|2018.6|''module load qiime2/2018.6''| | +|[[qiime2-software|qiime2]]|2019.10|''module load qiime2/2019.10''| | 
-|[[quast-software|quast]]|4.5|''module load quast/4.5''| |+|[[quast-software|quast]]|5.0.2|''module load quast/5.0.2''| | 
 +|[[quickmerge-software|quickmerge]]|0.3|''module load quickmerge/0.3''| |
 |[[quorum-software|Quorum]]|1.1.1|''module load quorum/1.1.1''| | |[[quorum-software|Quorum]]|1.1.1|''module load quorum/1.1.1''| |
-|[[r-software|R]]|3.5.2|''module load R/3.5''| |+|[[r-software|R]]|3.6.1|''module load R/3.6''| |
 |[[racon-software|racon]]|1.3.1|''module load racon/1.3.1''| | |[[racon-software|racon]]|1.3.1|''module load racon/1.3.1''| |
 |[[rmblast-software|rmblast]]|2.2.28|''module load rmblast/2.2.28''| | |[[rmblast-software|rmblast]]|2.2.28|''module load rmblast/2.2.28''| |
-|rapsearch|2.10|''module load rapsearch/2.10''| |+|[[rapsearch-software|rapsearch]]|2.22|''module load rapsearch/2.22''| |
 |[[ratt-software|RATT]]|r18|''module load ratt/r18''| | |[[ratt-software|RATT]]|r18|''module load ratt/r18''| |
 |[[raxml-software|RAxML]]|8.2.12|''module load RAxML/8.2.12''| | |[[raxml-software|RAxML]]|8.2.12|''module load RAxML/8.2.12''| |
Line 212: Line 241:
 |[[rdp-classifier-software|RDP Classifier]]|2.11|''module load rdp-classifier/2.11''| | |[[rdp-classifier-software|RDP Classifier]]|2.11|''module load rdp-classifier/2.11''| |
 |repeatmasker|4.0.5|''module load repeatmasker/4.0.5''| | |repeatmasker|4.0.5|''module load repeatmasker/4.0.5''| |
 +|[[repseqio-software|repseqio]]|1.3.3|''module load repseqio/1.3.3''| |
 |[[root-software|root]]|6.08.06|''module load root/6.08.06''| | |[[root-software|root]]|6.08.06|''module load root/6.08.06''| |
 |[[rrnaselector-software|rRNASelector]]|1.1|''module load rrnaselector/1.1''| | |[[rrnaselector-software|rRNASelector]]|1.1|''module load rrnaselector/1.1''| |
Line 217: Line 247:
 |[[rseqc-software|rseqc]]|2.6.4|''module load rseqc/2.6.4''| | |[[rseqc-software|rseqc]]|2.6.4|''module load rseqc/2.6.4''| |
 |[[ruby-software|ruby]]|2.2.3|''module load ruby/2.2.3''| | |[[ruby-software|ruby]]|2.2.3|''module load ruby/2.2.3''| |
-|[[samtools-software|samtools]]|1.8|''module load samtools/1.8''| |+|[[samtools-software|samtools]]|1.9|''module load samtools/1.9''| |
 |[[sailfish-software|sailfish]]|0.9.2|''module load sailfish/0.9.2''| | |[[sailfish-software|sailfish]]|0.9.2|''module load sailfish/0.9.2''| |
 |[[salmon-software|salmon]]|0.9.1|''module load salmon/0.9.1''| | |[[salmon-software|salmon]]|0.9.1|''module load salmon/0.9.1''| |
 |[[scipio-software|scipio]]|1.4.1|''module load scipio/1.4.1''| | |[[scipio-software|scipio]]|1.4.1|''module load scipio/1.4.1''| |
 |[[scythe-software|scythe]]|0.994-beta|''module load scythe/0.994-beta''| | |[[scythe-software|scythe]]|0.994-beta|''module load scythe/0.994-beta''| |
 +|[[sepp-software|sepp]]|4.3.8|''module load sepp/4.3.8''| |
 |[[seroba-software|seroba]]|1.0.0|''module load seroba/1.0.0''| | |[[seroba-software|seroba]]|1.0.0|''module load seroba/1.0.0''| |
 |seq_crumbs|0.1.8|''module load seq_crumbs/0.1.8''| | |seq_crumbs|0.1.8|''module load seq_crumbs/0.1.8''| |
-|[[seqkit-software|seqkit]]|0.7.2|''module load seqkit/0.7.2''| |+|[[seqkit-software|seqkit]]|0.11.0|''module load seqkit/0.11.0''| |
 |[[seqqs-software|seqqs]]|git-3d053750|''module load seqqs/git-3d053750''| | |[[seqqs-software|seqqs]]|git-3d053750|''module load seqqs/git-3d053750''| |
-|[[seqtk-software|seqtk]]|1.2-r102|''module load seqtk/1.2-r102''| |+|[[seqtk-software|seqtk]]|1.3|''module load seqtk/1.3''| |
 |[[shannon-software|shannon]]|0.0.2|''module load shannon/0.0.2''| | |[[shannon-software|shannon]]|0.0.2|''module load shannon/0.0.2''| |
 +|[[shasta-software|shasta]]|0.4.0|''module load shasta/0.4.0''| |
 |[[sickle-software|sickle]]|1.33|''module load sickle/1.33''| | |[[sickle-software|sickle]]|1.33|''module load sickle/1.33''| |
 |[[sift-software|sift]]|4.0.3b|''module load sift/4.0.3b''| | |[[sift-software|sift]]|4.0.3b|''module load sift/4.0.3b''| |
 |[[sistr-software|sistr]]|1.0.2|''module load sistr/1.0.2''| | |[[sistr-software|sistr]]|1.0.2|''module load sistr/1.0.2''| |
 |[[smalt-software|smalt]]|0.7.6|''module load smalt/0.7.6''| | |[[smalt-software|smalt]]|0.7.6|''module load smalt/0.7.6''| |
 +|[[smartdenovo-software|smartdenovo]]|git-5cc1356b|''module load smartdenovo/git-5cc1356b''| |
 +|[[snakemake-software|snakemake]]|5.7.0|''module load snakemake/5.7.0''| |
 |snowhite|1.1.4|''module load snowhite/1.1.4''| | |snowhite|1.1.4|''module load snowhite/1.1.4''| |
 |[[snpeff-software|SnpEff & SnpSift]]|4.1g|''module load snpeff/4.1g''| | |[[snpeff-software|SnpEff & SnpSift]]|4.1g|''module load snpeff/4.1g''| |
Line 247: Line 281:
 |splitstree|4.11.3|''module load splitstree/4.11.3''| | |splitstree|4.11.3|''module load splitstree/4.11.3''| |
 |spread|1.0.6|''module load spread/1.0.6''| | |spread|1.0.6|''module load spread/1.0.6''| |
-|[[sratoolkit-software|sratoolkit]]|2.8.2|''module load sratoolkit/2.8.2''| |+|[[squid-software|squid]]|1.9g|''module load squid/1.9g''| | 
 +|[[sratoolkit-software|sratoolkit]]|2.10.0|''module load sratoolkit/2.10.0''| |
 |[[sspace-software|sspace]]|3.0|''module load sspace/3.0''| | |[[sspace-software|sspace]]|3.0|''module load sspace/3.0''| |
 |[[sspace-longread-software|sspace-longread]]|1.1|''module load sspace-longread/1.1''| | |[[sspace-longread-software|sspace-longread]]|1.1|''module load sspace-longread/1.1''| |
 |[[stacks-software|stacks]]|1.24|''module load stacks/1.24''| | |[[stacks-software|stacks]]|1.24|''module load stacks/1.24''| |
 |staden|2.0.0b8|''module load staden/2.0.0b8''| | |staden|2.0.0b8|''module load staden/2.0.0b8''| |
-|[[star-software|star]]|2.5.3a|''module load star/2.5.3a''| |+|[[star-software|star]]|2.7.1a|''module load star/2.7.1a''| |
 |[[structure-software|structure]]|2.3.4|''module load structure/2.3.4'' | |[[structure-software|structure]]|2.3.4|''module load structure/2.3.4'' |
 |[[stringtie-software|stringtie]]|1.3.4d|''module load stringtie/1.3.4d''| | |[[stringtie-software|stringtie]]|1.3.4d|''module load stringtie/1.3.4d''| |
Line 278: Line 313:
 |[[velvet-software|velvet]]|1.2.10-kmer111|''module load velvet/1.2.10-kmer111''| | |[[velvet-software|velvet]]|1.2.10-kmer111|''module load velvet/1.2.10-kmer111''| |
 |[[vep-software|vep]]|92.1|''module load vep/92.1''| | |[[vep-software|vep]]|92.1|''module load vep/92.1''| |
-|[[vsearch-software|vsearch]]|2.8.0|''module load vsearch/2.8.0''| |+|[[viennarna-software|viennarna]]|2.4.14|''module load viennarna/2.4.14''| |
 |[[virusdetect-software|virusdetect]]|1.7|''module load virusdetect/1.7''| | |[[virusdetect-software|virusdetect]]|1.7|''module load virusdetect/1.7''| |
 |[[vntrseek-software|vntrseek]]|1.08|''module load vntrseek/1.08''| | |[[vntrseek-software|vntrseek]]|1.08|''module load vntrseek/1.08''| |
 +|[[vsearch-software|vsearch]]|2.8.0|''module load vsearch/2.8.0''| |
 |[[w2rap-software|w2rap]]|git-60781b6c|''module load w2rap/git-60781b6c''| | |[[w2rap-software|w2rap]]|git-60781b6c|''module load w2rap/git-60781b6c''| |
 |[[w2rap-contigger-software|w2rap-contigger]]|git-a43f5a05|''module load w2rap-contigger/git-a43f5a05''| | |[[w2rap-contigger-software|w2rap-contigger]]|git-a43f5a05|''module load w2rap-contigger/git-a43f5a05''| |
 |[[whatshap-software|whatshap]]|0.16|''module load whatshap/0.16''| | |[[whatshap-software|whatshap]]|0.16|''module load whatshap/0.16''| |
 |[[wise-software|wise]]|2.4.1|''module load wise/2.4.1''| | |[[wise-software|wise]]|2.4.1|''module load wise/2.4.1''| |
 +|[[wombat-software|wombat]]|2020-02-07|''module load wombat/2020-02-07''| |
 +|[[wtdbg2-software|wtdbg2]]|2.4|''module load wtdbg2/2.4''| |
  
 The source code for all environment modules can be found in [[https://github.com/ilri/hpc-environment-modules|ILRI's GitHub repository]]. The source code for all environment modules can be found in [[https://github.com/ilri/hpc-environment-modules|ILRI's GitHub repository]].
list-of-software.1552384128.txt.gz · Last modified: 2019/03/12 09:48 by jean-baka