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 the latest release or follow the instructions in the ReadTheDocs documentation.
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)
rdeval now supports PacBio CiFi data.
Using --cifi-enzyme, rdeval performs in-silico digestion of reads with a specified restriction enzyme motif.
Using --cifi-out-combinations, rdeval outputs all fragment combinations derived from each digested read.
Basic usage:
# Digest reads using enzyme motif
rdeval --cifi-enzyme DpnII cifi_reads.fastq -o testFiles/cifi_reads.digested.fastq
# Digest and output all PE combinations
rdeval --cifi-enzyme DpnII --cifi-out-combinations testFiles/cifi_reads.fastq -p rdeval_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:
Evaluation of sequencing reads at scale using rdeval.
Formenti G, Koo B, Sollitto M, Balacco J, Brajuka N, Burhans R, Duarte E, Giani AM, McCaffrey K, Medico JA, Myers EW, Smeds P, Nekrutenko A, Jarvis ED. Bioinformatics. 2025 Jul 22:btaf416
doi: https://doi.org/10.1093/bioinformatics/btaf416 PMID: 40694478