mebbert / pauvre

pauvre plotting software. originally designed for Oxford Nanopauvre data.

pauvre: a plotting package designed for nanopore reads

This package currently hosts one script for plotting.

• pauvre marginplot
  • takes a fastq file as input and outputs a marginal histogram with a heatmap.
• transparency is the default

Updates:

• 20170529 - added automatic scaling to the input fastq file. It scales to show the highest read quality and the top 99th percentile of reads by length.

Requirements

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

Installation

• 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 marginplot --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
  • 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 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)