Atlantool: a command line tool to retrieve DNA and RNA sequencing reads from BAM files by the read identifier.

ABSTRACT:

Motivation

DNA or RNA sequencing produce a large volume of data that is usually stored in a Binary Alignment Map (BAM) file format. Processing and analysis of this large genomic data require specialized software tools. The majority of processing requirements involve accessing DNA or RNA data by chromosomal co-ordinates using SAMtools or similar software. However, challenges arise where accessing the data by the sequencing read identifier is required, and as yet there is no reliable, efficient method or tool to do this. Here we present Atlantool, a fast software that can retrieve sequencing reads from a BAM file by the read identifier. Retrieval of sequencing reads using Atlantool requires a simple command line command similar to SAMtools. After a one-time creation of a read identif

SUBMITTER: Rath EM 

PROVIDER: S-EPMC12602190 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature