Source: transdecoder
Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
 Michael R. Crusoe <crusoe@debian.org>,
 Andreas Tille <tille@debian.org>,
Section: science
Build-Depends:
 debhelper-compat (= 13),
 liburi-perl,
 help2man,
 ncbi-blast+ <!nocheck>,
 hmmer <!nocheck>,
 r-base-core <!nocheck>,
 r-cran-ggplot2 <!nocheck>,
 r-bioc-seqlogo <!nocheck>,
 diamond-aligner <!nocheck>
Vcs-Browser: https://salsa.debian.org/med-team/transdecoder
Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git
Homepage: https://transdecoder.github.io/
Rules-Requires-Root: no

Package: transdecoder
Architecture: all
Depends:
 ${misc:Depends},
 ${perl:Depends},
 liburi-perl,
 r-base-core,
 python3,
Recommends:
 r-cran-ggplot2,
 r-bioc-seqlogo,
 diamond-aligner,
 hmmer,
Suggests:
 transdecoder-doc,
Description: find coding regions within RNA transcript sequences
 TransDecoder identifies candidate coding regions within transcript sequences,
 such as those generated by de novo RNA-Seq transcript assembly using Trinity,
 or constructed based on RNA-Seq alignments to the genome using Tophat and
 Cufflinks.
 .
 TransDecoder identifies likely coding sequences based on the following
 criteria:
  * a minimum length open reading frame (ORF) is found in a transcript sequence
  * a log-likelihood score similar to what is computed by the GeneID software
    is > 0.
  * the above coding score is greatest when the ORF is scored in the 1st
    reading frame as compared to scores in the other 5 reading frames.
  * if a candidate ORF is found fully encapsulated by the coordinates of
    another candidate ORF, the longer one is reported. However, a single
    transcript can report multiple ORFs (allowing for operons, chimeras, etc).
  * optional the putative peptide has a match to a Pfam domain above the noise
    cutoff score.

Package: transdecoder-doc
Architecture: all
Multi-Arch: foreign
Section: doc
Depends:
 ${misc:Depends},
 ${perl:Depends},
Description: find coding regions within transcripts
 TransDecoder identifies candidate coding regions within transcript sequences,
 such as those generated by de novo RNA-Seq transcript assembly using Trinity,
 or constructed based on RNA-Seq alignments to the genome using Tophat and
 Cufflinks.
 .
 TransDecoder identifies likely coding sequences based on the following
 criteria:
  * a minimum length open reading frame (ORF) is found in a transcript sequence
  * a log-likelihood score similar to what is computed by the GeneID software
    is > 0.
  * the above coding score is greatest when the ORF is scored in the 1st
    reading frame as compared to scores in the other 5 reading frames.
  * if a candidate ORF is found fully encapsulated by the coordinates of
    another candidate ORF, the longer one is reported. However, a single
    transcript can report multiple ORFs (allowing for operons, chimeras, etc).
  * optional the putative peptide has a match to a Pfam domain above the noise
    cutoff score.
 .
 This package contains the documentation and sample data.
