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list-of-software [2020/03/19 10:34] – aorthlist-of-software [2020/05/04 18:45] – aorth
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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''| |
-|[[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''| |
Line 55: Line 55:
 |[[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''| | |[[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]]|0.69-9|''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 78: 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''| |
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 |[[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''| | |[[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]]|1.10.0|''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''| | |[[igsimulator-software|igsimulator]]|git-c3778b74|''module load igsimulator/git-c3778b74''| |
Line 147: Line 149:
 |[[marginalign-software|marginalign]]|git-2369dafd|''module load marginalign/git-2369dafd''| | |[[marginalign-software|marginalign]]|git-2369dafd|''module load marginalign/git-2369dafd''| |
 |[[marginpolish-software|marginpolish]]|1.0.0|''module load marginpolish/1.0.0''| | |[[marginpolish-software|marginpolish]]|1.0.0|''module load marginpolish/1.0.0''| |
-|[[mash-software|mash]]|2.0|''module load mash/2.0''| |+|[[mash-software|mash]]|2.2|''module load mash/2.2''| |
 |[[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''| |
Line 166: Line 168:
 |[[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]]|3.0.11|''module load mixcr/3.0.11''| | |[[mixcr-software|mixcr]]|3.0.11|''module load mixcr/3.0.11''| |
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 |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''| |
Line 195: Line 198:
 |[[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''| | |[[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''| |
Line 215: Line 218:
 |[[presto-software|presto]]|0.5.13|''module load presto/0.5.13''| | |[[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''| |
 +|[[prinseq-software|prinseq]]|0.20.4|''module load prinseq/0.20.4''| |
 |[[prodigal-software|prodigal]]|2.6.3|''module load prodigal/2.6.3''| | |[[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''| |
-|[[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]]|2019.10|''module load qiime2/2019.10''| | |[[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''| | |[[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''| |
Line 228: Line 232:
 |[[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 273: Line 277:
 |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''| |
 +|[[squid-software|squid]]|1.9g|''module load squid/1.9g''| |
 |[[sratoolkit-software|sratoolkit]]|2.10.0|''module load sratoolkit/2.10.0''| | |[[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''| |
Line 304: Line 309:
 |[[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''| |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth