Package: trinityrnaseq (2.15.1+dfsg-5 and others)

[ Source: trinityrnaseq  ]

RNA-Seq De novo Assembly

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.

Other Packages Related to trinityrnaseq

• dep: berkeley-express

  Streaming quantification for high-throughput sequencing

• dep: bowtie

  Ultrafast memory-efficient short read aligner

• dep: bowtie2

  ultrafast memory-efficient short read aligner

• dep: default-jre-headless

  Standard Java or Java compatible Runtime (headless)

• dep: jaligner

  Smith-Waterman algorithm with Gotoh's improvement

• dep: jellyfish

  count k-mers in DNA sequences

• dep: kallisto

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• dep: libc6 (>= 2.34) [not alpha, ia64, sh4]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

  dep: libc6.1 (>= 2.37) [ia64]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, ppc64, ppc64el, x32]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sh4, sparc64]

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

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• dep: libgetopt-java

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• dep: libgomp1 (>= 6)

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• dep: libhts3 (>= 1.17) [not amd64, arm64, ppc64el, riscv64]

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• dep: libhts3t64 (>= 1.17) [amd64, arm64, ppc64el, riscv64]

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• dep: libjung-free-java

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• dep: libstdc++6 (>= 13.1)

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• dep: libunwind8 [ia64]

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• dep: liburi-perl

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• dep: ncbi-blast+

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• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-htseq

  Python3 high-throughput genome sequencing read analysis utilities

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• dep: rsem

  RNA-Seq by Expectation-Maximization

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: subread

  toolkit for processing next-gen sequencing data

• dep: trimmomatic

  flexible read trimming tool for Illumina NGS data

• dep: zlib1g (>= 1:1.1.4)

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• rec: curl

  command line tool for transferring data with URL syntax

• rec: gmap

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• rec: hisat2

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• rec: picard-tools

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• rec: r-bioc-biobase

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• rec: r-bioc-deseq2

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• rec: r-bioc-dexseq

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• rec: r-bioc-edger

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• rec: r-bioc-goseq

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• rec: r-bioc-rots

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• rec: r-cran-ape

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• rec: salmon

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• rec: tabix

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• rec: trinityrnaseq-examples

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• sug: collectl

  Utility to collect Linux performance data

• sug: r-bioc-tximport

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• sug: transdecoder

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Download trinityrnaseq

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.15.1+dfsg-2	1,656.3 kB	8,135.0 kB	[list of files]
amd64	2.15.1+dfsg-5+b1	1,679.8 kB	7,456.0 kB	[list of files]
arm64	2.15.1+dfsg-5+b1	1,616.8 kB	7,740.0 kB	[list of files]
ia64 (unofficial port)	2.15.1+dfsg-2	1,717.4 kB	9,611.0 kB	[list of files]
m68k (unofficial port)	2.15.1+dfsg-2	1,654.5 kB	7,399.0 kB	[list of files]
ppc64 (unofficial port)	2.15.1+dfsg-2	1,664.4 kB	8,572.0 kB	[list of files]
ppc64el	2.15.1+dfsg-5+b1	1,667.4 kB	8,316.0 kB	[list of files]
riscv64	2.15.1+dfsg-5+b1	1,660.8 kB	6,824.0 kB	[list of files]
sh4 (unofficial port)	2.15.1+dfsg-2	1,726.5 kB	7,736.0 kB	[list of files]
sparc64 (unofficial port)	2.15.1+dfsg-2	1,576.3 kB	18,081.0 kB	[list of files]
x32 (unofficial port)	2.15.1+dfsg-2	1,676.7 kB	7,287.0 kB	[list of files]