bafiq: BAM Flag Index Tool for Faster Repeated Queries of Mapped Reads

KOTRS, Jan a Matej LEXA. bafiq: BAM Flag Index Tool for Faster Repeated Queries of Mapped Reads. Online. In Workshop on Bioinformatics and Computational Biology (WCBC 2025). Telgárt, Slovakia: CEUR-WS.org, 2025, s. 334-342. ISSN 1613-0073.

Základní údaje

Originální název

bafiq: BAM Flag Index Tool for Faster Repeated Queries of Mapped Reads

Autoři

KOTRS, Jan a Matej LEXA

Vydání

Telgárt, Slovakia, Workshop on Bioinformatics and Computational Biology (WCBC 2025), od s. 334-342, 9 s. 2025

Nakladatel

CEUR-WS.org

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Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Slovensko

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/25:00143713

Organizační jednotka

Fakulta informatiky

ISSN

EID Scopus

2-s2.0-105033922577

Klíčová slova anglicky

NGS workflow; BAM flags; read alignment filtering; BAM index

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Anotace

V originále

We present bafiq, a command-line rust tool for repeated filtering and counting of sequencing reads stored in the BAM file format. This software can be easily incorporated into NGS computational workflows, especially in situations where one needs to repeatedly process mapped reads in large files based on their FLAG values. Commands in bafiq follow query language familiar from samtools and similar software where, however, indexing is only based on the location of reads in a reference genome. Our tool allows significant computational time savings in situations where a single BAM file is queried repeatedly based on different FLAG combinations, leveraging a flag-based index. We made an effort to match or outperform the commonly used samtools in sequence extraction tasks as well as in sequence counting tasks.