CITATION.cff

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cff-version: 1.2.0
title: >-
  BamToCov, an efficient toolkit for sequence
  coverage calculations
message: >-
  Please cite this dataset using the metadata from
  'preferred-citation'.
type: software
authors:
  - given-names: Andrea
    family-names: Telatin
    email: andrea.telatin@quadram.ac.uk
    affiliation: Quadram Institute Bioscience
    orcid: 'https://orcid.org/0000-0001-7619-281X'
  - given-names: Giovanni
    family-names: Birolo
    email: giovanni.birolo@unito.it
    affiliation: University of Turin
identifiers:
  - type: doi
    value: 10.1101/2021.11.12.466787
    description: >-
      BamToCov: an efficient toolkit for sequence
      coverage calculations
url: 'https://telatin.github.io/bamtocov/'
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 a
  memory efficient algorithm and is designed for
  integration in pipelines; this is possible as a
  result of reading 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
  also save the output in different formats (BED, Wig
  or counts). 

  The BamToCov algorithm can also handle
  strand-specific and/or physical coverage analyses.


  Availability: This program, accessory utilities,
  and their documentation are freely available at
  https://github.com/telatin/BamToCov.
keywords:
  - bioinformatics
  - sequence coverage
  - next-generation sequencing
license: MIT