edwardbetts / pauvre

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

Getting Started

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

Table of Contents

• Getting Started
• Users' Guide
• Installation
  • Requirements
  • Install Instructions
• Usage
  • pauvre stats
  • pauvre marginplot
    • Basic Usage
    • Plot Adjustments
    • Specialized Options
• Contributors

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
  • 
• 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
  • 

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
  • 

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
    • 

Contributors

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