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pauvre

Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

https://github.com/conchoecia/pauvre

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords from Contributors

bioinformatics genomics dna protein
Last synced: 11 months ago · JSON representation

Repository

Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

Basic Info
  • Host: GitHub
  • Owner: conchoecia
  • Language: C
  • Default Branch: master
  • Homepage:
  • Size: 2.24 MB
Statistics
  • Stars: 54
  • Watchers: 5
  • Forks: 13
  • Open Issues: 4
  • Releases: 2
Created about 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

travis-ci DOI

Getting Started

pauvre custommargin -i custom.tsv --ycol length --xcol qual # Custom tsv input

Table of Contents

Users' Guide

Pauvre is a plotting package originally designed to help QC the length and quality distribution of Oxford Nanopore or PacBio reads. The main outputs are marginplots. Now, pauvre also hosts other additional data plotting scripts.

This package currently hosts five scripts for plotting and/or printing stats.

  • pauvre marginplot
    • takes a fastq file as input and outputs a marginal histogram with a heatmap.
  • pauvre custommargin
    • takes a tsv as input and outputs a marginal histogram with custom columns of your choice.
  • 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
    • I am happy to introduce the redwood plot to the world as a 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. More details to follow as we document this program better...
  • 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.

Installation

Requirements

  • You must have the following installed on your system to install this software:
    • python 3.x
    • matplotlib
    • biopython
    • pandas
    • pillow

Install Instructions

  • Instructions to install on your mac or linux system. Not sure on Windows! Make sure python 3 is the active environment before installing.
    • git clone https://github.com/conchoecia/pauvre.git
    • cd ./pauvre
    • pip3 install .
  • Or, install with pip
    • pip3 install pauvre

Usage

stats

  • generate basic statistics about the fastq file. For example, if I want to know the number of bases and reads with AT LEAST a PHRED score of 5 and AT LEAST a read length of 500, run the program as below and look at the cells highlighted with <braces>.
    • pauvre stats --fastq miniDSMN15.fastq

``` numReads: 1000 numBasepairs: 1029114 meanLen: 1029.114 medianLen: 875.5 minLen: 11 maxLen: 5337 N50: 1278 L50: 296

                  Basepairs >= bin by mean PHRED and length

minLen Q0 Q5 Q10 Q15 Q17.5 Q20 Q21.5 Q25 Q25.5 Q30 0 1029114 1010681 935366 429279 143948 25139 3668 2938 2000 0 500 984212 <968653> 904787 421307 142003 24417 3668 2938 2000 0 1000 659842 649319 616788 300948 103122 17251 2000 2000 2000 0 et cetera... Number of reads >= bin by mean Phred+Len minLen Q0 Q5 Q10 Q15 Q17.5 Q20 Q21.5 Q25 Q25.5 Q30 0 1000 969 865 366 118 22 3 2 1 0 500 873 <859> 789 347 113 20 3 2 1 0 1000 424 418 396 187 62 11 1 1 1 0 et cetera... ```

marginplot

Basic Usage

  • automatically calls pauvre stats for each fastq file
  • Make the default plot showing the 99th percentile of longest reads
    • pauvre marginplot --fastq miniDSMN15.fastq
    • default
  • Make a marginal histogram for ONT 2D or 1D^2 cDNA data with a lower maxlen and higher maxqual.
    • pauvre marginplot --maxlen 4000 --maxqual 25 --lengthbin 50 --fileform pdf png --qualbin 0.5 --fastq miniDSMN15.fastq
    • example1

Plot Adjustments

  • Filter out reads with a mean quality less than 5, and a length less than 800. Zoom in to plot only mean quality of at least 4 and read length at least 500bp.
    • pauvre marginplot -f miniDSMN15.fastq --filt_minqual 5 --filt_minlen 800 -y --plot_minlen 500 --plot_minqual 4
    • test4

Specialized Options

  • Plot ONT 1D data with a large tail
    • pauvre marginplot --maxlen 100000 --maxqual 15 --lengthbin 500 <myfile>.fastq

  • Get more resolution on lengths

    • pauvre marginplot --maxlen 100000 --lengthbin 5 <myfile>.fastq

  • Turn off transparency if you just want a white background

    • pauvre marginplot --transparent False <myfile>.fastq
    • Note: transparency is the default behavior
    • transparency

Contributors

@conchoecia (Darrin Schultz) @mebbert (Mark Ebbert) @wdecoster (Wouter De Coster)

Owner

  • Name: darrin t schultz
  • Login: conchoecia
  • Kind: user
  • Location: Vienna, Austria
  • Company: University of Vienna

PhD from UC Santa Cruz Bioinformatics Department. Genome Assembly. Marine Invertebrates. Evolution.

GitHub Events

Total
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 2
  • Pull request event: 2
  • Fork event: 1
Last Year
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 2
  • Pull request event: 2
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 137
  • Total Committers: 8
  • Avg Commits per committer: 17.125
  • Development Distribution Score (DDS): 0.321
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
cypridina d****1@g****m 93
Wouter d****r@g****m 32
Ebbert m****3@r****u 6
Étienne Mollier e****r@d****g 2
Sam Nicholls s****n@s****k 1
Éric Araujo m****k@n****g 1
Étienne Mollier 6****r 1
Edward Betts e****d@4****m 1
Committer Domains (Top 20 + Academic)
4angle.com: 1 netwok.org: 1 studio8media.co.uk: 1 debian.org: 1 r5096855.mayo.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 33
  • Total pull requests: 16
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 20
  • Total pull request authors: 6
  • Average comments per issue: 2.67
  • Average comments per pull request: 0.56
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • conchoecia (9)
  • mebbert (3)
  • emollier (2)
  • ghost (2)
  • GeoMicroSoares (2)
  • Thuurslangen (1)
  • desmodus1984 (1)
  • dsladevt (1)
  • CarolineOhrman (1)
  • jpummil (1)
  • Tman3 (1)
  • alexiswl (1)
  • tillea (1)
  • abayega (1)
  • lfaller (1)
Pull Request Authors
  • emollier (6)
  • wdecoster (6)
  • mebbert (3)
  • EdwardBetts (1)
  • SamStudio8 (1)
  • merwok (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 71 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 4
    (may contain duplicates)
  • Total versions: 21
  • Total maintainers: 2
pypi.org: pauvre

Tools for plotting Oxford Nanopore and other long-read data.

  • Versions: 20
  • Dependent Packages: 1
  • Dependent Repositories: 4
  • Downloads: 71 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 1.2%
Dependent packages count: 4.7%
Dependent repos count: 7.5%
Average: 8.6%
Stargazers count: 9.6%
Forks count: 10.9%
Downloads: 17.7%
Maintainers (1)
cypridina
Last synced: 11 months ago
spack.io: py-pauvre

pauvre: plotting package designed for nanopore and PacBio long reads

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Stargazers count: 21.6%
Forks count: 24.5%
Average: 25.8%
Dependent packages count: 57.3%
Maintainers (1)
adamjstewart
Last synced: 11 months ago

Dependencies

setup.py pypi
  • biopython *
  • matplotlib *
  • numpy *
  • pandas *
  • scikit-learn *
  • scipy *