list-of-software
Differences
This shows you the differences between two versions of the page.
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list-of-software [2020/11/11 13:01] – aorth | list-of-software [2022/05/24 12:00] – aorth | ||
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|[[artemis-software|artemis]]|16.0.0|'' | |[[artemis-software|artemis]]|16.0.0|'' | ||
|[[augustus-software|augustus]]|3.3|'' | |[[augustus-software|augustus]]|3.3|'' | ||
- | |[[awscli-software|awscli]]|1.17.9|'' | + | |[[awscli-software|awscli]]|2.4.0|'' |
|[[bam-readcount-software|bam-readcount]]|0.8.0|'' | |[[bam-readcount-software|bam-readcount]]|0.8.0|'' | ||
|[[bamtools-software|bamtools]]|2.5.1|'' | |[[bamtools-software|bamtools]]|2.5.1|'' | ||
|[[barrnap-software|barrnap]]|0.9|'' | |[[barrnap-software|barrnap]]|0.9|'' | ||
|bayescan|2.1|'' | |bayescan|2.1|'' | ||
- | |[[bbmap-software|bbmap]]|38.67|'' | + | |[[bbmap-software|bbmap]]|38.95|'' |
- | |[[bcftools-software|bcftools]]|1.8|'' | + | |[[bcftools-software|bcftools]]|1.13|'' |
+ | |bcl2fastq|2.20.0.422|'' | ||
|[[beagle-software|beagle]]|3.1.2|'' | |[[beagle-software|beagle]]|3.1.2|'' | ||
|[[beast-software|beast]]|1.10.4|'' | |[[beast-software|beast]]|1.10.4|'' | ||
+ | |[[beast2-software|beast2]]|2.6.4|'' | ||
|[[bedops-software|bedops]]|2.4.29|'' | |[[bedops-software|bedops]]|2.4.29|'' | ||
|[[bedtools-software|bedtools]]|2.29.0|'' | |[[bedtools-software|bedtools]]|2.29.0|'' | ||
Line 39: | Line 41: | ||
|[[bitseq-software|bitseq]]|0.7.5|'' | |[[bitseq-software|bitseq]]|0.7.5|'' | ||
|[[blasr-software|blasr]]|smrtanalysis-4.0.0|'' | |[[blasr-software|blasr]]|smrtanalysis-4.0.0|'' | ||
- | |[[blast-software|blast]]|2.10.0+|'' | + | |[[blast-software|blast]]|2.12.0+|'' |
|[[blobtools-software|blobtools]]|0.9.19.3|'' | |[[blobtools-software|blobtools]]|0.9.19.3|'' | ||
|blat|06-Aug-2013|'' | |blat|06-Aug-2013|'' | ||
+ | |[[bmtagger-software|bmtagger]]|0.3.102.4|'' | ||
|[[bowtie-software|bowtie1 ]]|1.2.3|'' | |[[bowtie-software|bowtie1 ]]|1.2.3|'' | ||
|[[bowtie2-software|bowtie2 ]]|2.3.4.1|'' | |[[bowtie2-software|bowtie2 ]]|2.3.4.1|'' | ||
|[[brig-software|brig]]|0.95|'' | |[[brig-software|brig]]|0.95|'' | ||
- | |[[busco-software|BUSCO ]]|4.0.6|'' | + | |[[busco-software|BUSCO ]]|5.2.2|'' |
|[[bwa-software|bwa]]|0.7.17|'' | |[[bwa-software|bwa]]|0.7.17|'' | ||
|[[cafe-software|cafe]]|4.1|'' | |[[cafe-software|cafe]]|4.1|'' | ||
Line 51: | Line 54: | ||
|[[canu-software|canu]]|1.8|'' | |[[canu-software|canu]]|1.8|'' | ||
|cap3|latest|'' | |cap3|latest|'' | ||
- | |[[cd-hit-software|cd-hit]]|4.6.8|'' | + | |[[ccmetagen-software|ccmetagen]]|1.4.0|'' |
+ | |[[cd-hit-software|cd-hit]]|4.8.1|'' | ||
|[[cegma-software|cegma]]|v2.5|'' | |[[cegma-software|cegma]]|v2.5|'' | ||
|celera-wgs|6.1|'' | |celera-wgs|6.1|'' | ||
|censor|4.2.28|'' | |censor|4.2.28|'' | ||
- | |[[changeo-software|changeo]]|1.0.0|'' | + | |[[centrifuge-software|centrifuge]]|1.0.4|'' |
+ | |[[changeo-software|changeo]]|1.2.0|'' | ||
|[[checkm-software|checkm]]|1.1.2|'' | |[[checkm-software|checkm]]|1.1.2|'' | ||
|[[circos-software|circos]]|0.69-9|'' | |[[circos-software|circos]]|0.69-9|'' | ||
Line 68: | Line 73: | ||
|[[corset-software|corset]]|1.06|'' | |[[corset-software|corset]]|1.06|'' | ||
|cufflinks|2.2.1|'' | |cufflinks|2.2.1|'' | ||
- | |[[cutadapt-software|cutadapt]]|1.18|'' | + | |[[cutadapt-software|cutadapt]]|3.5|'' |
+ | |[[czid-cli-software|czid-cli]]|3.0.2|'' | ||
|[[dextractor-software|dextractor]]|git-a7f50c52|'' | |[[dextractor-software|dextractor]]|git-a7f50c52|'' | ||
|dendroscope|2.7.4|'' | |dendroscope|2.7.4|'' | ||
- | |[[diamond-software|diamond]]|0.9.9|'' | + | |[[diamond-software|diamond]]|2.0.14|'' |
|[[drep-software|drep]]|2.5.4|'' | |[[drep-software|drep]]|2.5.4|'' | ||
|[[ea-utils-software|ea-utils]]|1.04.807|'' | |[[ea-utils-software|ea-utils]]|1.04.807|'' | ||
|[[edirect-software|edirect]]| 7.80 | '' | |[[edirect-software|edirect]]| 7.80 | '' | ||
|eigenstrat|3.0|'' | |eigenstrat|3.0|'' | ||
+ | |[[emblmygff3-software|emblmygff3]]|2.1|'' | ||
|[[emboss-software|emboss]]|6.6.0|'' | |[[emboss-software|emboss]]|6.6.0|'' | ||
|[[easer-software|easer]]|1.7.0|'' | |[[easer-software|easer]]|1.7.0|'' | ||
Line 81: | Line 88: | ||
|[[exabayes-software|exabayes]]|1.4.1|'' | |[[exabayes-software|exabayes]]|1.4.1|'' | ||
|[[express-software|express]]|1.5.1|'' | |[[express-software|express]]|1.5.1|'' | ||
+ | |[[falco-software|falco]]|0.3.0|'' | ||
+ | |[[falcon-phase-software|falcon-phase]]|git-7c50154e|'' | ||
|[[fastANI-software|fastANI]]|1.3|'' | |[[fastANI-software|fastANI]]|1.3|'' | ||
+ | |[[fastp-software|fastp]]|0.22.0|'' | ||
|[[fastPHASE-software|fastPHASE]]|1.4.8|'' | |[[fastPHASE-software|fastPHASE]]|1.4.8|'' | ||
- | |[[fastqc-software|fastqc]]|0.11.7|'' | + | |[[fastqc-software|fastqc]]|0.11.9|'' |
|[[faststructure-software|fastSTRUCTURE]]|1.0|'' | |[[faststructure-software|fastSTRUCTURE]]|1.0|'' | ||
|[[fasttree-software|fasttree]]|2.1.11|'' | |[[fasttree-software|fasttree]]|2.1.11|'' | ||
Line 93: | Line 103: | ||
|[[flexbar-software|flexbar]]|2.7.0|'' | |[[flexbar-software|flexbar]]|2.7.0|'' | ||
|[[flux-capacitor-software|flux-capacitor]]|1.6.1|'' | |[[flux-capacitor-software|flux-capacitor]]|1.6.1|'' | ||
- | |[[flye-software|flye]]|2.8.1|'' | + | |[[flye-software|flye]]|2.9|'' |
|frappe|1.1|'' | |frappe|1.1|'' | ||
|[[fraggenescan-software|FragGeneScan ]]|1.30|'' | |[[fraggenescan-software|FragGeneScan ]]|1.30|'' | ||
- | |[[freebayes-software|FreeBayes | + | |[[freebayes-software|freebayes]]|1.3.4|'' |
+ | |[[funannotate-software|funannotate]]|1.8.9|'' | ||
|[[gassflow-software|GassFlow ]]|1.0|'' | |[[gassflow-software|GassFlow ]]|1.0|'' | ||
- | |[[gatk-software|GATK ]]|4.0.10.1|'' | + | |[[gatk-software|gatk]]|4.2.2.0|'' |
|[[gapfiller-software|gapfiller]]|1.10|'' | |[[gapfiller-software|gapfiller]]|1.10|'' | ||
|[[geneid-software|geneid]]|1.4.4|'' | |[[geneid-software|geneid]]|1.4.4|'' | ||
|[[genometools-software|genometools]]|1.6.1|'' | |[[genometools-software|genometools]]|1.6.1|'' | ||
+ | |[[genomeworks-software|genomeworks]]|git-baab5668|'' | ||
|[[genscan-software|genscan]]|latest|'' | |[[genscan-software|genscan]]|latest|'' | ||
|[[gffread-software|gffread]]|0.9.6|'' | |[[gffread-software|gffread]]|0.9.6|'' | ||
Line 107: | Line 119: | ||
|glu|1.0b3-prerelease4|'' | |glu|1.0b3-prerelease4|'' | ||
|[[gmap-software|gmap]]|2015-12-31|'' | |[[gmap-software|gmap]]|2015-12-31|'' | ||
+ | |[[graphlan-software|graphlan]]|1.1.3|'' | ||
|[[graphmap-software|graphmap]]|0.5.2|'' | |[[graphmap-software|graphmap]]|0.5.2|'' | ||
|[[grom-rd-software|grom-rd]]|1.0|'' | |[[grom-rd-software|grom-rd]]|1.0|'' | ||
Line 114: | Line 127: | ||
|[[gtdbtk-software|gtdbtk]]|1.1.1|'' | |[[gtdbtk-software|gtdbtk]]|1.1.1|'' | ||
|[[guidance-software|guidance]]|2.02|'' | |[[guidance-software|guidance]]|2.02|'' | ||
+ | |[[guppy-software|guppy]]|6.0.1|'' | ||
+ | |[[halcyon-software|halcyon]]|0.1.1|'' | ||
|[[hapflk-software|hapflk]]|1.4|'' | |[[hapflk-software|hapflk]]|1.4|'' | ||
|hapmix|2.0|'' | |hapmix|2.0|'' | ||
+ | |[[hawk-software|hawk]]|git-a177811d|'' | ||
+ | |[[hclust2-software|hclust2]]|1.0.0|'' | ||
|[[hdf5-software|hdf5]]|1.8.19|'' | |[[hdf5-software|hdf5]]|1.8.19|'' | ||
|[[hmmer-software|hmmer]]|3.3|'' | |[[hmmer-software|hmmer]]|3.3|'' | ||
+ | |[[hmmIBD-software|hmmIBD]]|2.0.4|'' | ||
|[[hpg-variant-software|hpg-variant]]|1.0|'' | |[[hpg-variant-software|hpg-variant]]|1.0|'' | ||
|[[hic_qc-software|hic_qc]]|git-1e132fb2|'' | |[[hic_qc-software|hic_qc]]|git-1e132fb2|'' | ||
+ | |[[hifiasm-software|hifiasm]]|0.16.1|'' | ||
|[[hisat2-software|hisat2]]|2.1.0|'' | |[[hisat2-software|hisat2]]|2.1.0|'' | ||
|[[htseq-software|htseq]]|0.9.1|'' | |[[htseq-software|htseq]]|0.9.1|'' | ||
- | |[[htslib-software|htslib]]|1.9|'' | + | |[[htslib-software|htslib]]|1.13|'' |
+ | |[[hypo-software|hypo]]|1.0.3|'' | ||
|[[idba-software|idba]]|1.1.2|'' | |[[idba-software|idba]]|1.1.2|'' | ||
|[[igblast-software|igblast]]|1.10.0|'' | |[[igblast-software|igblast]]|1.10.0|'' | ||
Line 128: | Line 148: | ||
|[[igrec-software|igrec]]|3.0.0|'' | |[[igrec-software|igrec]]|3.0.0|'' | ||
|[[igsimulator-software|igsimulator]]|git-c3778b74|'' | |[[igsimulator-software|igsimulator]]|git-c3778b74|'' | ||
- | |[[iqtree-software|iqtree]]|1.6.12|'' | + | |[[iqtree-software|iqtree]]|2.2.0|'' |
|[[igv-software|igv]]|2.4.5|'' | |[[igv-software|igv]]|2.4.5|'' | ||
|[[igvtools-software|igvtools]]|2.3.98|'' | |[[igvtools-software|igvtools]]|2.3.98|'' | ||
Line 134: | Line 154: | ||
|[[interproscan-software|interproscan]]|5.13|'' | |[[interproscan-software|interproscan]]|5.13|'' | ||
|i-tasser|latest|'' | |i-tasser|latest|'' | ||
+ | |[[ivar-software|ivar]]|1.3.1|'' | ||
|[[jellyfish-software|jellyfish]]|2.3.0|'' | |[[jellyfish-software|jellyfish]]|2.3.0|'' | ||
|jMHC|1.5.0929|'' | |jMHC|1.5.0929|'' | ||
|[[juicebox-software|juicebox]]|1.11.08|'' | |[[juicebox-software|juicebox]]|1.11.08|'' | ||
- | |[[kaiju-software|kaiju]]|1.4.4|'' | + | |[[juicer-software|juicer]]|1.6|'' |
+ | |[[kaiju-software|kaiju]]|1.8.2|'' | ||
|[[kallisto-software|kallisto]]|0.43.0|'' | |[[kallisto-software|kallisto]]|0.43.0|'' | ||
|[[karect-software|karect]]|1.0|'' | |[[karect-software|karect]]|1.0|'' | ||
|[[kat-software|kat]]|2.3.4|'' | |[[kat-software|kat]]|2.3.4|'' | ||
- | |[[kmc-software|kmc]]|3.0.0|'' | + | |[[kma-software|kma]]|1.4.0|'' |
+ | |[[kmc-software|kmc]]|3.1.1|'' | ||
|[[kmergenie-software|kmergenie]]|1.7038|'' | |[[kmergenie-software|kmergenie]]|1.7038|'' | ||
|[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | |[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|'' | ||
|[[kraken-software|kraken]]|2.0.8-beta|'' | |[[kraken-software|kraken]]|2.0.8-beta|'' | ||
- | |krona|2.4|'' | + | |[[krona-software|krona]]|2.8.1|'' |
|lamp|2.5|'' | |lamp|2.5|'' | ||
|lava|0.1|'' | |lava|0.1|'' | ||
Line 152: | Line 175: | ||
|[[lighter-software|lighter]]|1.1.2|'' | |[[lighter-software|lighter]]|1.1.2|'' | ||
|[[lordec-software|lordec]]|0.9|'' | |[[lordec-software|lordec]]|0.9|'' | ||
+ | |[[ltr_retriever-software|ltr_retriever]]|2.9.0|'' | ||
|lucy|1.19p|'' | |lucy|1.19p|'' | ||
- | |[[mafft-software|mafft]]|7.313|'' | + | |[[mafft-software|mafft]]|7.475|'' |
|[[maker-software|maker]]|3.01.03|'' | |[[maker-software|maker]]|3.01.03|'' | ||
|[[mapsplice-software|mapsplice]]|2.2.0|'' | |[[mapsplice-software|mapsplice]]|2.2.0|'' | ||
Line 164: | Line 188: | ||
|maximus|0.2|'' | |maximus|0.2|'' | ||
|[[mcl-software|mcl]]|14-137|'' | |[[mcl-software|mcl]]|14-137|'' | ||
+ | |[[mcscanx-software|mcscanx]]|git-97e74f40|'' | ||
|[[mecat-software|MECAT]]|git-d04bfa84|'' | |[[mecat-software|MECAT]]|git-d04bfa84|'' | ||
- | |[[medaka-software|medaka]]|0.8.2|'' | + | |[[medaka-software|medaka]]|1.4.3|'' |
- | |[[megahit-software|megahit]]|1.1.4|'' | + | |[[megahit-software|megahit]]|1.2.9|'' |
|megan|4.70.4|'' | |megan|4.70.4|'' | ||
|[[megax-software|megax]]|10.0.5|'' | |[[megax-software|megax]]|10.0.5|'' | ||
|[[metabat-software|metabat]]|2.12.1|'' | |[[metabat-software|metabat]]|2.12.1|'' | ||
- | |[[metaphlan2-software|metaphlan2]]|2.9.5|'' | + | |[[metaeuk-software|metaeuk]]|git-9818d1a5|'' |
+ | |[[metaphlan-software|metaphlan]]|3.0.13|'' | ||
|[[metis-software|metis]]|5.1.0|'' | |[[metis-software|metis]]|5.1.0|'' | ||
|[[migec-software|migec]]|1.2.4a|'' | |[[migec-software|migec]]|1.2.4a|'' | ||
|[[migmap-software|migmap]]|1.0.2|'' | |[[migmap-software|migmap]]|1.0.2|'' | ||
|[[miniasm-software|miniasm]]|0.3|'' | |[[miniasm-software|miniasm]]|0.3|'' | ||
- | |[[minimap2-software|minimap2]]|2.13|'' | + | |[[minimap2-software|minimap2]]|2.22|'' |
|[[minpath-software|MinPath]]|1.0.2|'' | |[[minpath-software|MinPath]]|1.0.2|'' | ||
|[[mira-software# | |[[mira-software# | ||
Line 188: | Line 214: | ||
|mpiblast|1.6.0|'' | |mpiblast|1.6.0|'' | ||
|mrbayes|3.2.2|'' | |mrbayes|3.2.2|'' | ||
- | |[[multiqc-software|multiqc]]|1.6|'' | + | |[[multiqc-software|multiqc]]|1.12|'' |
|[[muscle-software|muscle]]|3.8.1551|'' | |[[muscle-software|muscle]]|3.8.1551|'' | ||
|[[mummer-software|mummer]]|4.0.0rc1|'' | |[[mummer-software|mummer]]|4.0.0rc1|'' | ||
|[[nanopolish-software|nanopolish]]|0.10.2|'' | |[[nanopolish-software|nanopolish]]|0.10.2|'' | ||
|[[netmhcpan-software|netmhcpan]]|2.8|'' | |[[netmhcpan-software|netmhcpan]]|2.8|'' | ||
+ | |[[nextalign-software|nextalign]]|1.11.0|'' | ||
+ | |[[nextclade-software|nextclade]]|1.11.0|'' | ||
|[[nextclip-software|nextclip]]|1.3.1|'' | |[[nextclip-software|nextclip]]|1.3.1|'' | ||
- | |[[nextflow-software|nextflow]]|20.04.1|'' | + | |[[nextflow-software|nextflow]]|21.10 (21.10.6)|'' |
+ | |[[ngs-tools-software|ngs-tools]]|3.0.0|'' | ||
|[[ntcard-software|ntCard]]|1.0.0|'' | |[[ntcard-software|ntCard]]|1.0.0|'' | ||
|[[ngmlr-software|ngmlr]]|0.2.7|'' | |[[ngmlr-software|ngmlr]]|0.2.7|'' | ||
|[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | |[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|'' | ||
+ | |[[nQuire-software|nQuire]]|git-a990a88e|'' | ||
+ | |[[nvtop-software|nvtop]]|1.2.2|'' | ||
|novacraft|3.02.07|'' | |novacraft|3.02.07|'' | ||
|[[oases-software|oases]]|0.2.08|'' | |[[oases-software|oases]]|0.2.08|'' | ||
Line 209: | Line 240: | ||
|[[pandaseq-software|pandaseq]]|2.8.1|'' | |[[pandaseq-software|pandaseq]]|2.8.1|'' | ||
|[[pasta-software|pasta]]|d939adb2|'' | |[[pasta-software|pasta]]|d939adb2|'' | ||
+ | |[[pathoscope-software|pathoscope]]|2.0.7|'' | ||
|[[pear-software|pear]]|0.9.6|'' | |[[pear-software|pear]]|0.9.6|'' | ||
|[[pblat-software|pblat]]|2.1|'' | |[[pblat-software|pblat]]|2.1|'' | ||
Line 218: | Line 250: | ||
|[[phylip-software|phylip]]|3.696|'' | |[[phylip-software|phylip]]|3.696|'' | ||
|[[phyml-software|phyml]]|3.3.20180621|'' | |[[phyml-software|phyml]]|3.3.20180621|'' | ||
- | |[[picard-software|picard]]|2.17.0|'' | + | |[[picard-software|picard]]|2.26.1|'' |
|[[picrust-software# | |[[picrust-software# | ||
|[[pilon-software|pilon]]|1.23|'' | |[[pilon-software|pilon]]|1.23|'' | ||
Line 225: | Line 257: | ||
|[[plink-software|plink]]|2.00-alpha|'' | |[[plink-software|plink]]|2.00-alpha|'' | ||
|[[polyphen-software|polyphen]]|2.2.2|'' | |[[polyphen-software|polyphen]]|2.2.2|'' | ||
+ | |[[poplddecay-software|poplddecay]]|3.41|'' | ||
|[[porechop-software|porechop]]|0.2.4|'' | |[[porechop-software|porechop]]|0.2.4|'' | ||
|[[pplacer-software|pplacer]]|1.1.alpha19|'' | |[[pplacer-software|pplacer]]|1.1.alpha19|'' | ||
|[[prank-software|prank]]|170427|'' | |[[prank-software|prank]]|170427|'' | ||
|[[presto-software|presto]]|0.5.13|'' | |[[presto-software|presto]]|0.5.13|'' | ||
+ | |[[primalscheme-software|primalscheme]]|1.3.2|'' | ||
|primer3|2.3.6|'' | |primer3|2.3.6|'' | ||
|[[prinseq-software|prinseq]]|0.20.4|'' | |[[prinseq-software|prinseq]]|0.20.4|'' | ||
Line 234: | Line 268: | ||
|[[prokka-software|prokka]]|1.14.6|'' | |[[prokka-software|prokka]]|1.14.6|'' | ||
|[[provean-software|provean]]|1.1.5|'' | |[[provean-software|provean]]|1.1.5|'' | ||
- | |[[python-software|python]]|3.7.7|'' | + | |[[purge-haplotigs-software|purge_haplotigs]]|1.1.1|'' |
+ | |[[python-software|python]]|3.8.11|'' | ||
|qdd|3_beta|'' | |qdd|3_beta|'' | ||
|[[qiime-software|qiime]]|1.9.1|'' | |[[qiime-software|qiime]]|1.9.1|'' | ||
- | |[[qiime2-software|qiime2]]|2020.8|'' | + | |[[qiime2-software|qiime2]]|2021.8|'' |
|[[quast-software|quast]]|5.0.2|'' | |[[quast-software|quast]]|5.0.2|'' | ||
|[[quickmerge-software|quickmerge]]|0.3|'' | |[[quickmerge-software|quickmerge]]|0.3|'' | ||
|[[quorum-software|Quorum]]|1.1.1|'' | |[[quorum-software|Quorum]]|1.1.1|'' | ||
- | |[[r-software|R]]|3.6.1|'' | + | |[[r-software|R]]|4.2.0|'' |
|[[racon-software|racon]]|1.3.1|'' | |[[racon-software|racon]]|1.3.1|'' | ||
- | |[[rmblast-software|rmblast]]|2.10.0|'' | + | |[[rmblast-software|rmblast]]|2.11.0|'' |
|[[rapsearch-software|rapsearch]]|2.22|'' | |[[rapsearch-software|rapsearch]]|2.22|'' | ||
|[[ratt-software|RATT]]|r18|'' | |[[ratt-software|RATT]]|r18|'' | ||
Line 249: | Line 284: | ||
|[[ray-software|ray]]|2.3.1|'' | |[[ray-software|ray]]|2.3.1|'' | ||
|[[rdp-classifier-software|RDP Classifier]]|2.11|'' | |[[rdp-classifier-software|RDP Classifier]]|2.11|'' | ||
- | |[[repeatmasker-software|repeatmasker]]|4.1.1|'' | + | |[[recon-software|recon]]|1.08|'' |
+ | |[[repeatmasker-software|repeatmasker]]|4.1.2-p1|'' | ||
+ | |[[repeatmodeler-software|repeatmodeler]]|2.0.1|'' | ||
|[[repseqio-software|repseqio]]|1.3.3|'' | |[[repseqio-software|repseqio]]|1.3.3|'' | ||
|[[root-software|root]]|6.08.06|'' | |[[root-software|root]]|6.08.06|'' | ||
Line 256: | Line 293: | ||
|[[rseqc-software|rseqc]]|2.6.4|'' | |[[rseqc-software|rseqc]]|2.6.4|'' | ||
|[[ruby-software|ruby]]|2.2.3|'' | |[[ruby-software|ruby]]|2.2.3|'' | ||
- | |[[samtools-software|samtools]]|1.9|'' | + | |[[samtools-software|samtools]]|1.13|'' |
|[[sailfish-software|sailfish]]|0.9.2|'' | |[[sailfish-software|sailfish]]|0.9.2|'' | ||
|[[salmon-software|salmon]]|1.3.0|'' | |[[salmon-software|salmon]]|1.3.0|'' | ||
+ | |[[salsa-software|salsa]]|git-974589f3|'' | ||
+ | |[[satsuma2-software|satsuma2]]|git-37c5f386|'' | ||
|[[scipio-software|scipio]]|1.4.1|'' | |[[scipio-software|scipio]]|1.4.1|'' | ||
|[[scythe-software|scythe]]|0.994-beta|'' | |[[scythe-software|scythe]]|0.994-beta|'' | ||
- | |[[sepp-software|sepp]]|4.3.8|'' | + | |[[sepp-software|sepp]]|4.5.1|'' |
|[[seroba-software|seroba]]|1.0.0|'' | |[[seroba-software|seroba]]|1.0.0|'' | ||
|seq_crumbs|0.1.8|'' | |seq_crumbs|0.1.8|'' | ||
Line 275: | Line 314: | ||
|[[smalt-software|smalt]]|0.7.6|'' | |[[smalt-software|smalt]]|0.7.6|'' | ||
|[[smartdenovo-software|smartdenovo]]|git-5cc1356b|'' | |[[smartdenovo-software|smartdenovo]]|git-5cc1356b|'' | ||
- | |[[snakemake-software|snakemake]]|5.7.0|'' | + | |[[snakemake-software|snakemake]]|6.15.5|'' |
|[[sniffles-software|sniffles]]|1.0.12b|'' | |[[sniffles-software|sniffles]]|1.0.12b|'' | ||
|snowhite|1.1.4|'' | |snowhite|1.1.4|'' | ||
Line 287: | Line 326: | ||
|[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|'' | |[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|'' | ||
|[[solexaqa-software|SolexaQA++]]|3.1.3|'' | |[[solexaqa-software|SolexaQA++]]|3.1.3|'' | ||
- | |[[spades-software|spades]]|3.13.0|'' | + | |[[spades-software|spades]]|3.15 (3.15.4)|'' |
|[[sourmash-software|sourmash]]|1.0|'' | |[[sourmash-software|sourmash]]|1.0|'' | ||
|[[speedseq-software|speedseq]]|0.1.2|'' | |[[speedseq-software|speedseq]]|0.1.2|'' | ||
Line 294: | Line 333: | ||
|[[squid-software|squid]]|1.9g|'' | |[[squid-software|squid]]|1.9g|'' | ||
|[[sratoolkit-software|sratoolkit]]|2.10.0|'' | |[[sratoolkit-software|sratoolkit]]|2.10.0|'' | ||
+ | |[[sra-tools-software|sra-tools]]|3.0.0|'' | ||
+ | |[[srprism-software|srprism]]|3.1.2|'' | ||
|[[sspace-software|sspace]]|3.0|'' | |[[sspace-software|sspace]]|3.0|'' | ||
|[[sspace-longread-software|sspace-longread]]|1.1|'' | |[[sspace-longread-software|sspace-longread]]|1.1|'' | ||
Line 301: | Line 342: | ||
|[[structure-software|structure]]|2.3.4|'' | |[[structure-software|structure]]|2.3.4|'' | ||
|[[stringtie-software|stringtie]]|1.3.4d|'' | |[[stringtie-software|stringtie]]|1.3.4d|'' | ||
+ | |[[stringtie2-software|stringtie2]]|2.0.1|'' | ||
|[[subread-software|subread]]|1.6.2|'' | |[[subread-software|subread]]|1.6.2|'' | ||
|svmlight|V6.02|'' | |svmlight|V6.02|'' | ||
|tabix|git-76b4bbdf|'' | |tabix|git-76b4bbdf|'' | ||
|[[tablet-software|tablet]]|1.17.08.17|'' | |[[tablet-software|tablet]]|1.17.08.17|'' | ||
- | |[[tassel-software|tassel]]|4.0|'' | + | |[[tassel-software|tassel]]|5.2.77|'' |
|[[tmiseq-software|tmiseq]]|2016-01-31|'' | |[[tmiseq-software|tmiseq]]|2016-01-31|'' | ||
|[[tophat-software|tophat]]|2.1.0|'' | |[[tophat-software|tophat]]|2.1.0|'' | ||
Line 312: | Line 354: | ||
|[[transrate-software|Transrate]]|1.0.3|'' | |[[transrate-software|Transrate]]|1.0.3|'' | ||
|[[trf-software|trf]]|4.0.9|'' | |[[trf-software|trf]]|4.0.9|'' | ||
- | |[[trimmomatic-software|trimmomatic]]|0.38|'' | + | |[[trimgalore-software|trimgalore]]|0.6.7|'' |
+ | |[[trimmomatic-software|trimmomatic]]|0.39|'' | ||
|[[trinity-software|trinity]]|v2.11.0|'' | |[[trinity-software|trinity]]|v2.11.0|'' | ||
|[[trinotate-software|trinotate]]|2.0.2|'' | |[[trinotate-software|trinotate]]|2.0.2|'' | ||
Line 320: | Line 363: | ||
|[[usearch-software|usearch]]| v7.0.1090 |'' | |[[usearch-software|usearch]]| v7.0.1090 |'' | ||
|varscan|2.4.2|'' | |varscan|2.4.2|'' | ||
+ | |[[vcfdo-software|vcfdo]]|git-508cc19b|'' | ||
|[[vcflib-software|vcflib]]|git-7f1575e|'' | |[[vcflib-software|vcflib]]|git-7f1575e|'' | ||
- | |[[vcftools-software|vcftools]]|0.1.15|'' | + | |[[vcftools-software|vcftools]]|0.1.16|'' |
|[[velvet-software|velvet]]|1.2.10-kmer111|'' | |[[velvet-software|velvet]]|1.2.10-kmer111|'' | ||
+ | |[[velvetoptimiser-software|velvetoptimiser]]|2.2.6|'' | ||
|[[vep-software|vep]]|92.1|'' | |[[vep-software|vep]]|92.1|'' | ||
|[[vg-software|vg]]|1.27.0|'' | |[[vg-software|vg]]|1.27.0|'' |
list-of-software.txt · Last modified: 2024/06/19 11:50 by aorth