| abyss=1.9.0 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| augustus=3.2.2 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
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|
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| autoconf=latest |
|
|
Y |
|
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|
|
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|
|
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|
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|
|
| automake=latest |
|
|
Y |
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|
|
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|
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|
|
| bamtools=2.4.0 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
| bcftools=1.3.1 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
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|
|
Y |
|
Y |
Y |
|
Y |
| bedtools=2.25.0 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
| bioconductor-ballgown=2.2.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
| bioconductor-biobase=2.32.0 |
|
|
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|
Y |
| bioconductor-biobase=latest |
|
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|
Y |
|
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|
|
| bioconductor-biocgenerics=latest |
|
Y |
|
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|
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|
| bioconductor-biovizbase=1.18.0 |
|
|
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|
Y |
|
|
|
| bioconductor-cummerbund=2.12.1 |
|
|
|
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|
Y |
|
|
| bioconductor-cummerbund=2.16.0 |
|
|
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|
Y |
|
|
|
| bioconductor-dada2=1.0.3 |
|
|
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|
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|
|
|
Y |
|
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|
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|
|
| bioconductor-deseq2=1.10.1 |
|
|
|
|
|
|
Y |
|
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|
|
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|
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|
|
Y |
|
|
| bioconductor-deseq2=1.12.4 |
|
|
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|
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|
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|
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|
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|
Y |
|
|
|
| bioconductor-deseq=1.22.1 |
|
|
|
|
|
|
Y |
|
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|
|
|
|
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|
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|
|
Y |
|
|
| bioconductor-edger=3.14.0 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
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|
|
|
Y |
Y |
|
|
| bioconductor-genomicranges=1.26.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
Y |
|
|
|
| bioconductor-gviz=1.16.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
| bioconductor-s4vectors=0.12.0 |
|
|
|
|
|
|
|
|
|
|
|
|
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|
Y |
|
|
|
| blast=2.2.31 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
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|
|
Y |
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|
Y |
| blat=35 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
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|
|
Y |
|
Y |
Y |
|
Y |
| bowtie2=2.2.8 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
| bwa=0.7.15 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
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|
Y |
| cd-hit=4.6.4 |
|
|
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|
|
|
|
|
|
|
Y |
|
|
|
|
|
Y |
|
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|
|
| circos=0.69.2 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
|
|
|
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|
|
|
|
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|
|
| cmake=3.7.1 |
|
|
Y |
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
| cufflinks-patch=2.2.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
| cufflinks=2.2.1 |
|
|
|
|
|
|
Y |
|
|
|
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|
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|
|
Y |
|
Y |
| ddocent=2.1 |
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
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|
|
| deeptools=2.3.2 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
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|
|
| discovar=52488 |
|
|
|
Y |
|
|
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|
|
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|
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|
Y |
| discovardenovo=52488 |
|
|
|
Y |
|
|
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|
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|
|
|
|
|
|
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|
|
Y |
| fastqc=0.11.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
Y |
|
|
|
| fastx_toolkit=0.0.14 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
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|
|
| freebayes=1.0.2.29 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
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|
Y |
| gatk=3.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
Y |
| gatk=3.6 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
| gcc=latest |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| genblasta=1.0.4 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| genblastg=1.38 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
| hisat2=2.0.4 |
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
| hmmer=3.1b2 |
Y |
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
| htseq=0.6.1.post1 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
Y |
Y |
|
|
| idba=1.1.1 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
| ipython=latest |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
| jellyfish=2.2.3 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| kallisto=0.43.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
Y |
|
|
| kat=2.0.8 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| kmergenie=1.7016 |
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| kraken=0.10.6_eaf8fb68 |
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
| libgcc=latest |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| m4=latest |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| macs2=2.1.1.20160309 |
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| mafft=7.221 |
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
| mawk=1.3.4 |
|
|
|
|
|
Y |
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
| mcl=14.137 |
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
| metaphlan2=2.5.0 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| metavelvet-sl-feature-extraction=1.0 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| metavelvet-sl=1.0 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| metavelvet=1.1.01 |
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| mira=4.0.2 |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| mothur=1.36.1 |
|
|
|
|
|
Y |
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
| multiqc=0.8 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
| numpy=1.11.1 |
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| numpy=latest |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
| pauda=1.0.1 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| pear=0.9.6 |
|
|
|
Y |
|
Y |
Y |
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
Y |
| perl-app-cpanminus=latest |
Y |
Y |
Y |
Y |
|
|
|
|
|
Y |
|
Y |
|
|
|
|
|
|
|
|
|
Y |
| perl-biox-workflow-plugin-filedetails=0.11 |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
|
Y |
|
|
Y |
Y |
Y |
Y |
Y |
Y |
| perl-biox-workflow-plugin-fileexists=0.13 |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
| perl-biox-workflow=1.10 |
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
| perl-dbi=latest |
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
| perl-hpc-runner-command=3.1.1 |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
|
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
Y |
| perl-termreadkey=latest |
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
| picard=2.0.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
| picard=2.5.0 |
|
|
|
Y |
|
Y |
Y |
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
Y |
| prinseq=0.20.4 |
|
|
|
Y |
|
Y |
Y |
|
|
|
|
|
|
|
|
|
|
|
Y |
Y |
|
Y |
| pyfaidx=0.4.7.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
| pyfasta=0.5.2 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
| pyfastaq=3.11.0 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
| python=2.7 |
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| python=3.5 |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
| python=latest |
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
| qiime=1.9.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
| qualimap=2.2.2a |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
| quast=4.1 |
|
|
|
Y |
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| r-base=3.3.1 |
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
Y |
|
|
Y |
| r-cairo=latest |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
| r-essentials=latest |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
Y |
|
|
Y |
| r-ggplot2=latest |
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| r=3.3.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
|
| rainbow=2.0.4 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
|
|
|
|
| repeatmasker=4.0.6 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| rmblast=2.2.28 |
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| rsem=1.2.28 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
Y |
|
| salmon=0.6.0 |
|
|
|
|
|
|
Y |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| samtools=1.3.1 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
| scipy=latest |
|
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|
Y |
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|
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| seqtk=1.2 |
|
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|
Y |
|
Y |
Y |
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|
Y |
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|
Y |
|
Y |
Y |
|
Y |
| sickle=0.5 |
|
|
|
Y |
|
|
Y |
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|
|
| snpeff=4.3 |
Y |
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Y |
| snpsift=4.3 |
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|
Y |
| soapdenovo2-gapcloser=1.12 |
|
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|
Y |
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| soapdenovo2-prepare=2.0 |
|
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|
|
Y |
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|
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| soapdenovo2=2.40 |
|
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|
Y |
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|
| spades=3.9.0 |
|
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|
Y |
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| stacks=1.40 |
|
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|
Y |
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| star=2.5.2a |
|
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|
Y |
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|
Y |
Y |
|
Y |
| stringtie=1.3.0 |
|
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|
Y |
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|
| tophat=2.1.0 |
Y |
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|
Y |
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|
Y |
Y |
|
Y |
| transdecoder=2.1.0 |
Y |
|
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|
Y |
|
| trimmomatic=0.35 |
|
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|
|
Y |
|
|
| trimmomatic=0.36 |
|
|
|
Y |
|
Y |
Y |
|
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|
|
Y |
|
|
|
|
Y |
|
|
|
| trinity=2.2.0 |
|
|
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|
|
|
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|
|
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|
|
Y |
|
| trinotate=3.0.1 |
Y |
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|
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|
|
Y |
|
| vcflib=1.0.0_rc1 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
| vcftools=0.1.14 |
Y |
|
|
Y |
|
Y |
Y |
Y |
|
|
Y |
|
|
|
|
|
Y |
|
Y |
Y |
|
Y |
| velvet=1.2.10 |
|
|
|
Y |
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|
|
| zlib=latest |
|
|
Y |
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|