pauvre: a plotting package designed for nanopore and PacBio long reads
This package currently hosts four scripts for plotting and/or printing stats.
- takes a fastq file as input and outputs a marginal histogram with a heatmap.
- 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
- 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
.bamfiles for the long reads and RNAseq data, and a
.gfffile for the annotation. More details to follow as we document this program better...
- 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
- 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
.gfffile per circular genome and one directory of gene alignments.
- 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
- 20171130 - v0.1.86 - some changes by @wdecoster to integrate
pauvreinto nanoplot, as well as some formatting changes that may make
pauvrework better with python2.7. Adding Travis-CI functionality.
- 20171025 - v0.1.83 - added some changes to make marginplot interface
with @wdecoster's nanoPlot
package, and made
pauvre statsonly output data tables for filtered reads.
pauvre statsalso now has the
- 20171018 - v0.1.8 - you can now filter reads and adjust the plotting viewing window. See below for a demonstration. I added the following options:
--filt_maxlen FILT_MAXLEN This sets the max read length filter reads. --filt_maxqual FILT_MAXQUAL This sets the max mean read quality to filter reads. --filt_minlen FILT_MINLEN This sets the min read length to filter reads. --filt_minqual FILT_MINQUAL This sets the min mean read quality to filter reads. --plot_maxlen PLOT_MAXLEN Sets the maximum viewing area in the length dimension. --plot_maxqual PLOT_MAXQUAL Sets the maximum viewing area in the quality dimension. --plot_minlen PLOT_MINLEN Sets the minimum viewing area in the length dimension. --plot_minqual PLOT_MINQUAL Sets the minimum viewing area in the quality dimension.
- 20171014 - uploading information on
- 20171012 - made
pauvre statsmore consistently produce useful histograms.
pauvre statsnow also calculates some statistics for different size ranges.
- 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.
- You must have the following installed on your system to install this software:
- python 3.x
- Instructions to install on your mac or linux system. Not sure on
Windows! Make sure python 3 is the active environment before
git clone https://github.com/conchoecia/pauvre.git
pip3 install .
- Or, install with pip
pip3 install pauvre
- 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
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...
- automatically calls
pauvre statsfor each fastq file
- Make the default plot showing the 99th percentile of longest reads
- Make a marginal histogram for ONT 2D or 1D^2 cDNA data with a lower maxlen and higher maxqual.
Filter reads and adjust viewing window
- 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.
- 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
@conchoecia (Darrin Schultz) @mebbert (Mark Ebbert) @wdecoster (Wouter De Coster)