Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow.
BMC Bioinformatics
; 24(1): 164, 2023 Apr 24.
Article
em En
| MEDLINE
| ID: mdl-37095442
ABSTRACT
BACKGROUND:
Massively parallel sequencing includes many liquid handling steps which introduce the possibility of sample swaps, mixing, and duplication. The unique profile of inherited variants in human genomes allows for comparison of sample identity using sequence data. A comparison of all samples vs. each other (all vs. all) provides both identification of mismatched samples and the possibility of resolving swapped samples. However, all vs. all comparison complexity grows as the square of the number of samples, so efficiency becomes essential.RESULTS:
We have developed a tool for fast all vs. all genotype comparison using low level bitwise operations built into the Perl programming language. Importantly, we have also developed a complete workflow allowing users to start with either raw FASTQ sequence files, aligned BAM files, or genotype VCF files and automatically generate comparison metrics and summary plots. The tool is freely available at https//github.com/teerjk/TimeAttackGenComp/ .CONCLUSIONS:
A fast and easy to use method for genotype comparison as described here is an important tool to ensure high quality and robust results in sequencing studies.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Sequenciamento de Nucleotídeos em Larga Escala
Limite:
Humans
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
Estados Unidos