Commands in the package
BubbleUpClusteringChrysalisCreateIwormFastaBundleFastaToDeBruijnGraphFromFastaQuantifyGraphReadsToTranscriptsTrinityfastaToKmerCoverageStatsinchworm
About trinityrnaseq
From Debian's package description
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.
From Debian's description of the trinityrnaseq package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libgomp1libhts3t64libstdc++6zlib1gperljalignerlibgetopt-javalibjung-free-javabowtiebowtie2libwww-perldefault-jre-headlesssamtoolsjellyfishr-base-corersemberkeley-expresstrimmomaticparaflyncbi-blast+python3liburi-perlpython3-htseqsubreadkallisto
Recommends
curltrinityrnaseq-examplespicard-toolstabixgmapsalmonrna-starhisat2r-cran-tidyverser-cran-readrr-bioc-edgerr-bioc-deseq2r-bioc-rotsr-cran-clusterr-cran-fastclusterr-bioc-ctcr-bioc-goseqr-cran-goplotr-cran-gplotsr-bioc-dexseqr-cran-aper-bioc-biobaser-bioc-qvaluer-cran-argparser-cran-kernsmoothpython3-numpypython3-hisat2
Related apps
- rsemRNA-Seq by Expectation-MaximizationCommand line
- salmonwicked-fast transcript quantification from RNA-seq dataCommand line
- raconconsensus module for raw de novo DNA assembly of long uncorrected readsCommand line
- velvetoptimiserautomatically optimise Velvet do novo assembly parametersCommand line
rockhopperguiSystem for analyzing bacterial RNA-seq data- kallistonear-optimal RNA-Seq quantificationCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the trinityrnaseq package, under that package's license.
- Description: Debian's description of the trinityrnaseq package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.