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list-of-software [2019/12/09 08:55] – aorthlist-of-software [2020/04/06 15:18] – 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''| |
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 |[[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''| |
Line 53: Line 54:
 |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]]|0.3.9|''module load changeo/0.3.9''| |
 +|[[checkm-software|checkm]]|1.1.2|''module load checkm/1.1.2''| |
 |[[circos-software|circos]]|0.67|''module load circos/0.67''| | |[[circos-software|circos]]|0.67|''module load circos/0.67''| |
 |[[clonalframe-software|clonalframe]]|1.2|''module load clonalframe/1.2''| | |[[clonalframe-software|clonalframe]]|1.2|''module load clonalframe/1.2''| |
Line 67: 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'' | |
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 |[[flye-software|flye]]|2.4.2|''module load flye/2.4.2''| | |[[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''| |
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 |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]]|0.9.1|''module load htseq/0.9.1''| | |[[htseq-software|htseq]]|0.9.1|''module load htseq/0.9.1''| |
 |[[htslib-software|htslib]]|1.9|''module load htslib/1.9''| | |[[htslib-software|htslib]]|1.9|''module load htslib/1.9''| |
 +|[[idba-software|idba]]|1.1.2|''module load idba/1.1.2''| |
 |[[igblast-software|igblast]]|1.6.0|''module load igblast/1.6.0''| | |[[igblast-software|igblast]]|1.6.0|''module load igblast/1.6.0''| |
 |[[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''| |
 |[[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''| |
Line 145: Line 150:
 |[[masurca-software|masurca]]|3.3.1|''module load masurca/3.3.1''| | |[[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''| |
Line 153: Line 159:
 |[[megax-software|megax]]|10.0.5|''module load megax/10.0.5''| | |[[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 174: Line 181:
 |[[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]]|19.10.0|''module load nextflow/19.10.0''| |
 |[[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''| |
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 |[[plink-software|plink]]|2.00-alpha|''module load plink/2.00-alpha''| | |[[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''| |
 +|[[prodigal-software|prodigal]]|2.6.3|''module load prodigal/2.6.3''| |
 |[[prokka-software|prokka]]|1.11|''module load prokka/1.11''| | |[[prokka-software|prokka]]|1.11|''module load prokka/1.11''| |
 |[[provean-software|provean]]|1.1.5|''module load provean/1.1.5''| | |[[provean-software|provean]]|1.1.5|''module load provean/1.1.5''| |
Line 210: Line 221:
 |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]]|2019.7|''module load qiime2/2019.7''| |+|[[qiime2-software|qiime2]]|2019.10|''module load qiime2/2019.10''| |
 |[[quast-software|quast]]|4.5|''module load quast/4.5''| | |[[quast-software|quast]]|4.5|''module load quast/4.5''| |
 |[[quickmerge-software|quickmerge]]|0.3|''module load quickmerge/0.3''| | |[[quickmerge-software|quickmerge]]|0.3|''module load quickmerge/0.3''| |
Line 223: Line 234:
 |[[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 239: Line 251:
 |[[seqtk-software|seqtk]]|1.3|''module load seqtk/1.3''| | |[[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]]|0.3.0|''module load shasta/0.3.0''| |+|[[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''| |
Line 299: Line 311:
 |[[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''| | |[[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.txt · Last modified: 2024/06/19 11:50 by aorth