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Coval specifications


Unique identifier OMICS_14832
Name Coval
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data SAM/BAM alignment data
Output data The called SNPs/indels.
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.5
Stability Stable
Maintained Yes



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  • person_outline Shunichi Kosugi <>

Publication for Coval

Coval in publications

PMCID: 5790050
PMID: 29398946
DOI: 10.1270/jsbbs.17061

[…] quality score of <20 were excluded from the analysis. the cleaned reads were aligned to the reference genome of yuikogane using bwa aligner (version 0.7.15). after aligning the short reads, the coval software (version 1.2) was used for filtering out mismatched reads and for variant calling (). the snp-index was defined as the ratio between the number of reads of shinanotsubuhime snp […]

PMCID: 5604175
PMID: 28927400
DOI: 10.1186/s12915-017-0419-x

[…] p4- and p3-specific heterozygous positions, the illumina reads from the two bulk-sequenced samples (male and female bulks) were aligned to the reference sequences using bwa [] and subjected to coval filtering [] as previously described. when the p3 reference sequence was used for alignment, the snp-index values were calculated only at all of the p4-specific heterozygous positions. […]

PMCID: 5506652
PMID: 28028892
DOI: 10.1111/pbi.12686

[…] parent (gpbd 4) were first aligned to the above‐mentioned reference tetraploid genome assembly using inbuilt bwa aligner. after aligning sequence reads to both diploid genomes separately, the coval software was used for postprocessing and filtering of the alignment files (kosugi et al., ). the variants were called between resistant parent (gpbd 4) and both diploid reference genomes. […]

PMCID: 5288901
PMID: 28148242
DOI: 10.1186/s12864-017-3511-2

[…] were detected, and the average values were calculated by sliding window analysis. the “window size” was configured from 100 kbp to 1 mbp, and “slide size” was set to 10 kbp. the snp-calling filter “coval” [] was set to 6. next, snp positions with a snp index of <0.3 were excluded, and a threshold of more than seven mismatches and a depth of fewer than four were eliminated, as these snps may […]

PMCID: 5248594
PMID: 27774740
DOI: 10.1111/jipb.12505

[…] (q) score <20. after data pre‐processing, clean reads were aligned to the williams 82 reference sequence using bwa (li and durbin ) software, and the aligned short reads were filtered with coval to improve snp calling accuracy. snp identification was performed using the genome analysis toolkit (gatk, mckenna et al. ) and samtools (li et al. ). a detailed description of the protocol […]

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Coval institution(s)
Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; Kazusa DNA Research Institute, Kisarazu, Chiba, Japan; The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
Coval funding source(s)
This work was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN), the Ministry of Agriculture, Forestry, and Fisheries of Japan and Grant-in-aid for Scientific Research from the Ministry of Education, Cultures, Sports and Technology, Japan (Grant-in-Aid for Scientific Research on Innovative Areas 23113009) and by JSPS KAKENHI Grant Number 22510217; and by the Gatsby Charitable Foundation.

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