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Source: pinfish
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Nilesh Patra <nilesh@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-golang,
golang-any,
golang-github-biogo-biogo-dev,
golang-github-biogo-hts-dev,
golang-github-google-uuid-dev,
samtools,
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/pinfish
Vcs-Git: https://salsa.debian.org/med-team/pinfish.git
Homepage: https://github.com/nanoporetech/pinfish
Rules-Requires-Root: no
XS-Go-Import-Path: github.com/nanoporetech/pinfish
Package: pinfish
Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends},
minimap2,
racon
Description: Collection of tools to annotate genomes using long read transcriptomics data
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
Package: pinfish-examples
Architecture: all
Depends: ${misc:Depends},
${shlibs:Depends}
Description: Examples and test data for pinfish
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
.
This package contains a test data set as well as sample scripts
running some test suite provided by Debian also as autopkgtest.
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