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list-of-software [2023/07/07 09:06] – aorthlist-of-software [2023/10/12 09:07] – aorth
Line 44: Line 44:
 |[[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]]|2.12.0+|''module load blast/2.12.0+''| |+|[[blast-software|blast]]|2.14.1+|''module load blast/2.14.1+''| |
 |[[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-software|blat]]|37x1|''module load blat/37x1''| | |[[blat-software|blat]]|37x1|''module load blat/37x1''| |
Line 60: Line 60:
 |[[cd-hit-software|cd-hit]]|4.8.1|''module load cd-hit/4.8.1''| | |[[cd-hit-software|cd-hit]]|4.8.1|''module load cd-hit/4.8.1''| |
 |[[cegma-software|cegma]]|v2.5|''module load cegma/v2.5''| | |[[cegma-software|cegma]]|v2.5|''module load cegma/v2.5''| |
 +|[[cgmlst-dists-software|cgmlst-dists]]|0.4.0|''module load cgmlst-dists/0.4.0''| |
 |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''| |
Line 65: Line 66:
 |[[changeo-software|changeo]]|1.2.0|''module load changeo/1.2.0''| | |[[changeo-software|changeo]]|1.2.0|''module load changeo/1.2.0''| |
 |[[checkm-software|checkm]]|1.1.2|''module load checkm/1.1.2''| | |[[checkm-software|checkm]]|1.1.2|''module load checkm/1.1.2''| |
 +|[[chewbbaca-software|chewbbaca]]|git-87102063|''module load chewbbaca/git-87102063''| |
 |[[circos-software|circos]]|0.69-9|''module load circos/0.69-9''| | |[[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''| |
-|[[clustalo-software|clustalo]]|1.2.3|''module load clustalo/1.2.3''| | 
 |clustalw|2.1|''module load clustalw/2.1''| | |clustalw|2.1|''module load clustalw/2.1''| |
 |[[cnvnator-software|CNVnator]]|0.3.3|''module load CNVnator/0.3.3''| | |[[cnvnator-software|CNVnator]]|0.3.3|''module load CNVnator/0.3.3''| |
Line 81: Line 82:
 |dendroscope|2.7.4|''module load dendroscope/2.7.4''| | |dendroscope|2.7.4|''module load dendroscope/2.7.4''| |
 |[[diamond-software|diamond]]|2.0.14|''module load diamond/2.0.14''| | |[[diamond-software|diamond]]|2.0.14|''module load diamond/2.0.14''| |
 +|[[disty-software|disty]]|0.1.0|''module load disty/0.1.0''| |
 +|[[dorado-software|dorado]]|0.3.4|''module load dorado/0.3.4''| |
 |[[drep-software|drep]]|2.5.4|''module load drep/2.5.4''| | |[[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''| |
Line 102: Line 105:
 |[[fasttree-software|fasttree]]|2.1.11|''module load fasttree/2.1.11''| | |[[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''| |
 +|[[figaro-software|figaro]]|git-337aa9|''module load figaro/git-337aa9''| |
 |figtree|1.4.0|''module load figtree/1.4.0''| | |figtree|1.4.0|''module load figtree/1.4.0''| |
 |[[flapjack-software|flapjack ]]|1.18.04.23-beta|''module load flapjack/1.18.04.23-beta''| | |[[flapjack-software|flapjack ]]|1.18.04.23-beta|''module load flapjack/1.18.04.23-beta''| |
Line 171: Line 175:
 |[[kma-software|kma]]|1.4.11|''module load kma/1.4.11''| | |[[kma-software|kma]]|1.4.11|''module load kma/1.4.11''| |
 |[[kmc-software|kmc]]|3.1.1|''module load kmc/3.1.1''| | |[[kmc-software|kmc]]|3.1.1|''module load kmc/3.1.1''| |
 +|[[kmerfreq-software|kmerfreq]]|git-90fca00d|''module load kmerfreq/git-90fca00d''| |
 |[[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''| |
Line 184: Line 189:
 |[[ltr_retriever-software|ltr_retriever]]|2.9.0|''module load ltr_retriever/2.9.0''| | |[[ltr_retriever-software|ltr_retriever]]|2.9.0|''module load ltr_retriever/2.9.0''| |
 |lucy|1.19p|''module load lucy/1.19p''| | |lucy|1.19p|''module load lucy/1.19p''| |
-|[[mafft-software|mafft]]|7.475|''module load mafft/7.475''| |+|[[mafft-software|mafft]]|7.505|''module load mafft/7.505''| |
 |[[maker-software|maker]]|3.01.03|''module load maker/3.01.03''| | |[[maker-software|maker]]|3.01.03|''module load maker/3.01.03''| |
 |[[mapsplice-software|mapsplice]]|2.2.0|''module load mapsplice/2.2.0''| | |[[mapsplice-software|mapsplice]]|2.2.0|''module load mapsplice/2.2.0''| |
Line 203: Line 208:
 |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| | |[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| |
 |[[metaeuk-software|metaeuk]]|git-9818d1a5|''module load metaeuk/git-9818d1a5''| | |[[metaeuk-software|metaeuk]]|git-9818d1a5|''module load metaeuk/git-9818d1a5''| |
-|[[metaphlan-software|metaphlan]]|3.0.13|''module load metaphlan/3.0.13''| |+|[[metaphlan-software|metaphlan]]|4.0.6|''module load metaphlan/4.0.6''| |
 |[[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 222: Line 227:
 |[[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-software|mrbayes]]|3.2.7a|''module load mrbayes/3.2.7a''| |
 |[[multiqc-software|multiqc]]|1.12|''module load multiqc/1.12''| | |[[multiqc-software|multiqc]]|1.12|''module load multiqc/1.12''| |
 |[[muscle-software|muscle]]|3.8.1551|''module load muscle/3.8.1551''|  | |[[muscle-software|muscle]]|3.8.1551|''module load muscle/3.8.1551''|  |
Line 231: Line 236:
 |[[nextclade-software|nextclade]]|2.11.0|''module load nextclade/2.11.0''| | |[[nextclade-software|nextclade]]|2.11.0|''module load nextclade/2.11.0''| |
 |[[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]]|22.10 (22.10.8)|''module load nextflow/22.10''| |+|[[nextflow-software|nextflow]]|23.04 (23.04.2)|''module load nextflow/23.04''| |
 |[[ngs-tools-software|ngs-tools]]|3.0.0|''module load ngs-tools/3.0.0''| | |[[ngs-tools-software|ngs-tools]]|3.0.0|''module load ngs-tools/3.0.0''| |
 |[[ntcard-software|ntCard]]|1.0.0|''module load ntCard/1.0.0''| | |[[ntcard-software|ntCard]]|1.0.0|''module load ntCard/1.0.0''| |
Line 248: Line 253:
 |[[pairfq-software|pairfq]]|0.14.4|''module load pairfq/0.14.4''| | |[[pairfq-software|pairfq]]|0.14.4|''module load pairfq/0.14.4''| |
 |[[paml-software|paml]]|4.9a|''module load paml/4.9a''| | |[[paml-software|paml]]|4.9a|''module load paml/4.9a''| |
 +|[[panaroo-software|panaroo]]|1.3.3|''module load panaroo/1.3.3''| |
 |[[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''|  |
Line 286: Line 292:
 |[[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''| |
-|[[r-software|R]]|4.3.0|''module load R/4.3''| |+|[[r-software|R]]|4.3.1|''module load R/4.3''| |
 |[[racon-software|racon]]|1.5.0|''module load racon/1.5.0''| | |[[racon-software|racon]]|1.5.0|''module load racon/1.5.0''| |
 |[[rapsearch-software|rapsearch]]|2.22|''module load rapsearch/2.22''| | |[[rapsearch-software|rapsearch]]|2.22|''module load rapsearch/2.22''| |
Line 300: Line 306:
 |[[rgi-software|rgi]]|6.0.2|''module load rgi/6.0.2''| | |[[rgi-software|rgi]]|6.0.2|''module load rgi/6.0.2''| |
 |[[rmblast-software|rmblast]]|2.11.0|''module load rmblast/2.11.0''| | |[[rmblast-software|rmblast]]|2.11.0|''module load rmblast/2.11.0''| |
 +|[[roary-software|roary]]|3.13.0|''module load roary/3.13.0''| |
 |[[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 321: Line 328:
 |[[shannon-software|shannon]]|0.0.2|''module load shannon/0.0.2''| | |[[shannon-software|shannon]]|0.0.2|''module load shannon/0.0.2''| |
 |[[shannon_cpp-software|shannon_cpp]]|0.5.0|''module load shannon_cpp/0.5.0''| | |[[shannon_cpp-software|shannon_cpp]]|0.5.0|''module load shannon_cpp/0.5.0''| |
 +|[[shapeit-software|shapeit]]|2.904|''module load shapeit/2.904''| |
 |[[shasta-software|shasta]]|0.4.0|''module load shasta/0.4.0''| | |[[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''| |
Line 349: Line 357:
 |[[sra-tools-software|sra-tools]]|3.0.0|''module load sra-tools/3.0.0''| | |[[sra-tools-software|sra-tools]]|3.0.0|''module load sra-tools/3.0.0''| |
 |[[srprism-software|srprism]]|3.1.2|''module load srprism/3.1.2''| | |[[srprism-software|srprism]]|3.1.2|''module load srprism/3.1.2''| |
 +|[[srst2-software|srst2]]|git-73f885f5|''module load srst2/git-73f885f5''| |
 |[[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''| |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth