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.
Either download one of the releases or git clone https://github.com/vgl-hub/kreeq.git --recursive and make -j in the kreeq folder.
kreeq validate -f input.[fasta|fastq][.gz] -r reads1.fastq[.gz] reads2.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 -r testFiles/random1.fastq
Importantly, the kreeq database can only be computed once on the read set, and reused for multiple analyses to save runtime:
kreeq validate -r testFiles/random1.fastq -o db.kreeq
kreeq validate -f testFiles/random1.fasta -d db.kreeq
Similarly, kreeq databases can be generated separately for multiple inputs and combined, with increased performance in HPC environments:
kreeq validate -r testFiles/random1.fastq -o random1.kreeq
kreeq validate -r testFiles/random2.fastq -o random2.kreeq
kreeq union -d random1.kreeq random2.kreeq -o union.kreeq
kreeq validate -f testFiles/random1.fasta -d union.kreeq
The output of kreeq can be tabled as .bed, .csv or as highly compressed .kwig or .bkwig (binary kwig), the latter can then be reinflated with the utility kreeq-decompress:
kreeq validate -f testFiles/random1.fasta -r testFiles/random1.fastq -o test.kwig
kreeq validate -f testFiles/random1.fasta -r testFiles/random1.fastq -o test.bkwig
kreeq-decompress test.bkwig --expand | python mycoolscript.py
Kreeq can also generate a vcf of candidate variants, which can be used for correction:
kreeq validate -f testFiles/to_correct.fasta -d testFiles/test1.kreeq -o candidate_errors.vcf
bgzip -c candidate_errors.vcf > candidate_errors.vcf.gz
tabix -pvcf candidate_errors.vcf.gz
bcftools consensus -f testFiles/to_correct.fasta candidate_errors.vcf.gz > corrected.fasta
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