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

Area of Science:

• Genomics
• Bioinformatics

Background:

• DNA/RNA sequencing generates large datasets, typically stored in Binary Alignment Map (BAM) files.
• Current tools efficiently access genomic data by chromosomal coordinates but lack methods for retrieval by sequencing read identifier.

Purpose of the Study:

• To present Atlantool, a novel software designed for rapid retrieval of sequencing reads from BAM files using read identifiers.
• To address the need for an efficient tool to access specific records in large genomic datasets.

Main Methods:

• Atlantool utilizes a command-line interface, similar to SAMtools.
• A one-time index creation of read identifiers is performed, using the BGZF format compatible with BAM files.

Main Results:

• Atlantool enables instantaneous retrieval of sequencing reads by their unique identifier.
• The software efficiently handles sequencing reads of any length.

Conclusions:

• Atlantool provides a reliable and efficient solution for accessing specific sequencing reads within large BAM files.
• This tool facilitates new possibilities for genomic data analysis and research.