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Paketti: trinityrnaseq (2.5.1+dfsg-2)

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.

Muut pakettiin trinityrnaseq liittyvät paketit

  • depends
  • recommends
  • suggests
  • 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: curl
    command line tool for transferring data with URL syntax
  • 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: libc6 (>= 2.14)
    GNU C Library: Shared libraries
    myös näennäispaketti, jonka toteuttaa libc6-udeb
  • dep: libcommons-collections4-java
    Apache Commons Collections - Extended Collections API for Java
  • dep: libgcc1 (>= 1:3.0)
    GCC support library
  • dep: libgetopt-java
    GNU getopt - Java port
  • dep: libgomp1 (>= 4.9)
    GCC OpenMP (GOMP) support library
  • dep: libhts2 (>= 1.0)
    C library for high-throughput sequencing data formats
  • dep: libjung-free-java
    Java Universal Network/Graph Framework
  • dep: libstdc++6 (>= 5.2)
    GNU Standard C++ Library v3
  • dep: libwww-perl
    simple and consistent interface to the world-wide web
  • dep: parafly
    parallel command processing using OpenMP
  • dep: perl
    Larry Wall's Practical Extraction and Report Language
  • dep: python
    interactive high-level object-oriented language (default version)
  • dep: r-base-core
    GNU R core of statistical computation and graphics system
  • dep: r-bioc-qvalue
    GNU R package for Q-value estimation for FDR control
  • dep: r-cran-cluster
    GNU R package for cluster analysis by Rousseeuw et al
  • dep: rsem
    RNA-Seq by Expectation-Maximization
  • dep: samtools
    processing sequence alignments in SAM and BAM formats
  • dep: transdecoder
    find coding regions within RNA transcript sequences
  • dep: trimmomatic
    flexible read trimming tool for Illumina NGS data
  • sug: collectl
    Utility to collect Linux performance data

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