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bamtocov

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

https://github.com/telatin/bamtocov

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
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    Links to: joss.theoj.org, zenodo.org
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  • ○
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  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary

Keywords

alignment bam bed bioinformatics coverage gff ngs
Last synced: 6 months ago · JSON representation ·

Repository

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

Basic Info
Statistics
  • Stars: 63
  • Watchers: 3
  • Forks: 7
  • Open Issues: 2
  • Releases: 12
Topics
alignment bam bed bioinformatics coverage gff ngs
Created about 5 years ago · Last pushed 8 months ago
Metadata Files
Readme Contributing License Citation

README.md

bamtocov

Build Bamtocov Downloads Platforms Paper

bamtocov logo

Tools to extract coverage informations from BAM (and CRAM) files, based on the covtobed algorithm that supports stranded coverage and physical coverage, input from streams and uses a memory-efficient algorithm.

:book: Documentation

Full documentation is available online at the :book: dedicated website, or in this repository under docs.

Installation

The BamToCov package is available from :package: BioConda

bash conda install -y -c bioconda bamtocov

Benchmarks

Bamtocov has the smallest memory footprint of any other coverage tool, while maintaining reasonable speeds

See also

Initially we also used Lapper, and I recommend checking out this library for fast interval operations.

Cite

Giovanni Birolo, Andrea Telatin, BamToCov: an efficient toolkit for sequence coverage calculations, Bioinformatics, 2022

Owner

  • Name: Andrea Telatin
  • Login: telatin
  • Kind: user
  • Location: Norwich, UK
  • Company: Quadram Institute Bioscience

Bioinformatician @quadram-institute-bioscience

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

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

GitHub Events

Total
  • Issues event: 3
  • Watch event: 5
  • Issue comment event: 2
  • Push event: 6
  • Fork event: 1
Last Year
  • Issues event: 3
  • Watch event: 5
  • Issue comment event: 2
  • Push event: 6
  • Fork event: 1

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