A general purpose, multithreaded read analysis and manipulation tool.
rdeval is a single, fast and exhaustive tool for summary statistics and simultaneous manipulation of sequence read files in fa*[.gz], bam, and cram formats. rdeval also allows seamless file conversion between formats.
Typical metrics include:
- number of reads
- total read length
- average read length
- read N50
- shortest read
- longest read
- coverage
- GC content
- base composition
Either download one of the releases or git clone https://github.com/vgl-hub/rdeval.git --recursive and make -j in the rdeval folder.
rdeval input.fa*[.gz]|bam|cram|rd [expected genome size]
To check out all options and flags use rdeval -h.
You can test some typical usage with the files in the testFiles folder, e.g.:
rdeval testFiles/random1.fastq 10 // computes summary statistics, including coverage (expected genome size 10bp)
Additional documentation for rdeval is available in ReadTheDocs.
Rdeval is part of the gfastar tool suite. If you use rdeval in your work, please cite:
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristo Gallardo, Alice Giani, Olivier Fedrigo, Erich D. Jarvis