kreeq
k-mer analysis quality evaluation tool
kreeq is a single fast kmer-based QV computation tool for genome assemblies. It computes both the kmers and the QV on the fly. The kmer counting capabilities are inherited from kcount.
Installation
Either download one of the releases or git clone https://github.com/vgl-hub/kreeq.git --recursive and make -j in the kreeq folder.
Usage
kreeq validate -f input.[fasta|fastq][.gz] -r reads.fastq[.gz] [-k 21]
It accepts multiple read files as input, separated by space. To check out all options and flags use kreeq -h.
You can test some typical usage with the files in the testFiles folder, e.g.:
kreeq validate -f testFiles/random1.fasta testFiles/random1.fastq
How to cite
This tool is part of the gfastar tool suite. If you use kreeq 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