Atlantool: a command line tool to retrieve DNA and RNA sequencing reads from BAM files by the read identifier
Year: 2024
Type: article
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 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/.
Source: Bioinformatics Advances
Authors: Emma M Rath, Huy Le, Yukhym Pyshnohraiev, Amitdev Ranjitdev, Robin Stocker, Alex Yakovlev, Congenital Heart Disease Synergy Study Group, Sally L Dunwoodie, David S Winlaw, Eleni Giannoulatou, Natasha Nassar, Edwin Kirk, Gavin Chapman, Gillian Blue, Gary Sholler, Samantha Lain, David S Winlaw, Sally L Dunwoodie, Eleni Giannoulatou
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,917
Funders: Victor Chang Cardiac Research Institute, National Computational Infrastructure, Children’s Hospital of Wisconsin Research Institute, Murdoch Children's Research Institute, NSW Ministry of Health, Medical Research Council, National Health and Medical Research Council, National Cancer Institute
Awards: G2956611489, Preparing Australia for Genomic Medicine: A proposal by the Australian Genomics Health Alliance, Identifying genetic and environmental factors that cause NAD deficiency and disrupt embryogenesis, Improving the genetic diagnosis of cardiovascular disease, Towards a Mechanistic Understanding of the Causes of Congenital Heart Disease and Associated Extra-Cardiac Anomalies
OpenAlex ID: W4414466210