Year: 2022
Type: article
Abstract: MOTIVATION: Many genomics applications require the computation of nucleotide coverage of a reference genome or the ability to determine how many reads map to a reference region. RESULTS: BamToCov is a toolkit for rapid and flexible coverage computation that relies on the most memory efficient algorithm and is designed for integration in pipelines, given its ability to read alignment files from streams. The tools in the suite can process sorted BAM or CRAM files, allowing the user to extract coverage information via different filtering approaches and to save the output in different formats (BED, Wig or counts). The BamToCov algorithm can also handle strand-specific and/or physical coverage analyses. AVAILABILITY AND IMPLEMENTATION: This program, accessory utilities and their documentation are freely available at https://github.com/telatin/BamToCov. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics
Authors: Giovanni Birolo, Andrea Telatin
Institutions: University of Turin, Norwich Research Park, Quadram Institute
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,618
Awards: G1217252016, Quadram Institute Bioscience UKRI Innovation Fellowships: BBSRC Flexible Talent Mobility Accounts, Changes in gut microbe-host interactions and their impact beyond the gut, G3302311078, G3870339886, G5377849018, BRinging Artificial INTelligencE home for a better cAre of amyotrophic lateral sclerosis and multiple SclERosis, G6394911336, CLIMB-BIG-DATA: A Cloud Infrastructure for Big-Data Microbial Bioinformatics, G7305703845, Determinants of microbe-host responses in the gut across life, G917981861
OpenAlex ID: W4212972500