python3-pauvre

QC and genome browser plotting Oxford Nanopore and PacBio long reads

Description

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.

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