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

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 identifier index in the same BGZF format as BAM files, retrieval of data by the read identifier appears to be instantaneous. The sequencing reads can be of any length. Atlantool fills the existing need for a reliable tool to efficiently retrieve specific records from high volume DNA or RNA sequencing data and will enable new genomic analyses to be envisaged and carried out. Availability and implementation: Precompiled Atlantool executables are freely available for download from https://github.com/VCCRI/atlantool/releases for Linux, macOS, and Windows platforms, as is a Java JAR file that permits Atlantool to run in a Java environment. The source code and user documentation are available at https://github.com/VCCRI/atlantool/.