Source: python-pauvre
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Build-Depends: debhelper-compat (= 12),
dh-python,
python3,
python3-setuptools,
python3-matplotlib <!nocheck>,
python3-biopython <!nocheck>,
python3-pandas <!nocheck>,
python3-numpy <!nocheck>,
python3-scipy <!nocheck>,
python3-sklearn <!nocheck>,
python3-progressbar <!nocheck>
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/python-pauvre
Vcs-Git: https://salsa.debian.org/med-team/python-pauvre.git
Homepage: https://github.com/conchoecia/pauvre
Package: python3-pauvre
Architecture: all
Section: python
Depends: ${python3:Depends},
${misc:Depends},
python3-matplotlib,
python3-biopython,
python3-pandas,
python3-numpy,
python3-scipy,
python3-sklearn
Description: QC and genome browser plotting Oxford Nanopore and PacBio long reads
Pauvre is a plotting package designed for nanopore and PacBio long reads.
.
This package currently hosts four scripts for plotting and/or printing stats.
.
pauvre marginplot
Takes a fastq file as input and outputs a marginal histogram with a
heatmap.
pauvre stats
Takes a fastq file as input and prints out a table of stats, including
how many basepairs/reads there are for a length/mean quality cutoff.
This is also automagically called when using pauvre marginplot
pauvre redwood
Method of representing circular genomes. A redwood plot contains long
reads as "rings" on the inside, a gene annotation "cambrium/phloem",
and a RNAseq "bark". The input is .bam files for the long reads and
RNAseq data, and a .gff file for the annotation.
pauvre synteny
Makes a synteny plot of circular genomes. Finds the most parsimonius
rotation to display the synteny of all the input genomes with the
fewest crossings-over. Input is one .gff file per circular genome
and one directory of gene alignments.