rdeval
A general purpose, multithreaded read analysis and manipulation tool.
rdeval is a single, fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq [.gz]) read file manipulation. rdeval also allows seamless fasta<>fastq[.gz] conversion.
Typical fast* metrics include:
- number of reads
- total read length
- average read length
- read N50
- shortest read
- longest read
- coverage
- GC content
- base composition
Installation
Either download one of the releases or git clone https://github.com/vgl-hub/rdeval.git --recursive and make -j in the rdeval folder.
Usage
`rdeval input.[fasta|fastq][.gz] [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)
How to cite
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