Gonomics: uniting high performance and readability for genomics with Go.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 08 2023
01 08 2023
Historique:
received:
23
03
2023
revised:
19
07
2023
medline:
31
8
2023
pubmed:
25
8
2023
entrez:
25
8
2023
Statut:
ppublish
Résumé
Many existing software libraries for genomics require researchers to pick between competing considerations: the performance of compiled languages and the accessibility of interpreted languages. Go, a modern compiled language, provides an opportunity to address this conflict. We introduce Gonomics, an open-source collection of command line programs and bioinformatic libraries implemented in Go that unites readability and performance for genomic analyses. Gonomics contains packages to read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, and VCF), and can convert and interface between these formats. Furthermore, our modular library structure provides a flexible platform for researchers developing their own software tools to address specific questions. These commands can be combined and incorporated into complex pipelines to meet the growing need for high-performance bioinformatic resources. Gonomics is implemented in the Go programming language. Source code, installation instructions, and documentation are freely available at https://github.com/vertgenlab/gonomics.
Identifiants
pubmed: 37624924
pii: 7251027
doi: 10.1093/bioinformatics/btad516
pmc: PMC10466080
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NHGRI NIH HHS
ID : R35 HG011332
Pays : United States
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
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