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list-of-software [2023/09/28 08:54] – aorthlist-of-software [2023/12/18 08:55] – aorth
Line 26: Line 26:
 |[[artic-software|artic]]|1.2.3|''module load artic/1.2.3''| | |[[artic-software|artic]]|1.2.3|''module load artic/1.2.3''| |
 |[[artic-tools-software|artic-tools]]|0.3.1|''module load artic-tools/0.3.1''| | |[[artic-tools-software|artic-tools]]|0.3.1|''module load artic-tools/0.3.1''| |
 +|[[aspera-cli-software|aspera-cli]]|4.15.0|''module load aspera-cli/4.15.0''| |
 |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| | |[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| |
 |[[awscli-software|awscli]]|2.4.0|''module load awscli/2''| | |[[awscli-software|awscli]]|2.4.0|''module load awscli/2''| |
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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]]|2.12.0+|''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 61:
 |[[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''| |
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 |[[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]]|3.2.0|''module load chewbbaca/3.2.0''| |+|[[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''| |
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 |[[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''| | |[[disty-software|disty]]|0.1.0|''module load disty/0.1.0''| |
-|[[dorado-software|dorado]]|0.3.4|''module load dorado/0.3.4''| |+|[[dorado-software|dorado]]|0.5.0|''module load dorado/0.5.0''| |
 |[[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 161: Line 163:
 |[[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''| | |[[infernal-software|infernal]]|1.1.2|''module load infernal/1.1.2''| |
 +|[[integron-finder-software|integron-finder]]|2.0.2|''module load integron-finder/2.0.2''| |
 |[[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 226: Line 229:
 |[[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''| |
-|[[mrbays-software|mrbayes]]|3.2.7a|''module load mrbayes/3.2.7a''| |+|[[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''|  |
 |[[mummer-software|mummer]]|4.0.0rc1|''module load mummer/4.0.0rc1''| | |[[mummer-software|mummer]]|4.0.0rc1|''module load mummer/4.0.0rc1''| |
 |[[nanopolish-software|nanopolish]]|0.14.0|''module load nanopolish/0.14.0''| | |[[nanopolish-software|nanopolish]]|0.14.0|''module load nanopolish/0.14.0''| |
 +|[[nanoqc-software|nanoqc]]|git-a7bcbdce|''module load nanoqc/git-a7bcbdce''| |
 |[[netmhcpan-software|netmhcpan]]|2.8|''module load netmhcpan/2.8''| | |[[netmhcpan-software|netmhcpan]]|2.8|''module load netmhcpan/2.8''| |
 |[[nextalign-software|nextalign]]|1.11.0|''module load nextalign/1.11.0''| | |[[nextalign-software|nextalign]]|1.11.0|''module load nextalign/1.11.0''| |
 |[[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]]|23.04 (23.04.2)|''module load nextflow/23.04''| |+|[[nextflow-software|nextflow]]|23.10 (23.10.0)|''module load nextflow/23.10''| |
 |[[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 241: Line 245:
 |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|''module load ngsqctoolkit/2.3.3''| | |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|''module load ngsqctoolkit/2.3.3''| |
 |[[nQuire-software|nQuire]]|git-a990a88e|''module load nQuire/git-a990a88e''| | |[[nQuire-software|nQuire]]|git-a990a88e|''module load nQuire/git-a990a88e''| |
-|[[nvtop-software|nvtop]]|2.0.2|''module load nvtop/2.0.2''| | 
 |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''| |
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 |[[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]]|2.00-alpha|''module load plink/2.00-alpha''| | |[[plink-software|plink]]|2.00-alpha|''module load plink/2.00-alpha''| |
 +|[[pod5-software|pod5]]|0.3.2|''module load pod5/0.3.2''| |
 |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| | |[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| |
 |[[poplddecay-software|poplddecay]]|3.41|''module load poplddecay/3.41''| | |[[poplddecay-software|poplddecay]]|3.41|''module load poplddecay/3.41''| |
Line 305: Line 309:
 |[[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''| |
 |[[rsem-software|RSEM]]|1.3.1|''module load RSEM/1.3.1''| | |[[rsem-software|RSEM]]|1.3.1|''module load RSEM/1.3.1''| |
 |[[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]]|3.1 (3.1.4)|''module load ruby/3.1''| |
 |[[samtools-software|samtools]]|1.15.1|''module load samtools/1.15.1''| | |[[samtools-software|samtools]]|1.15.1|''module load samtools/1.15.1''| |
 |[[sailfish-software|sailfish]]|0.9.2|''module load sailfish/0.9.2''| | |[[sailfish-software|sailfish]]|0.9.2|''module load sailfish/0.9.2''| |
Line 363: Line 368:
 |[[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''| |
-|[[stringtie2-software|stringtie2]]|2.0.1|''module load stringtie2/2.0.1''| |+|[[stringtie2-software|stringtie2]]|2.2.1|''module load stringtie2/2.2.1''| |
 |[[subread-software|subread]]|1.6.2|''module load subread/1.6.2''| | |[[subread-software|subread]]|1.6.2|''module load subread/1.6.2''| |
 |svmlight|V6.02|''module load svmlight/V6.02''| | |svmlight|V6.02|''module load svmlight/V6.02''| |
list-of-software.txt · Last modified: 2024/05/15 09:52 by aorth