bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files

Pierre Lindenbaum (1) , Richard Redon (1)

1 ITX - ITX - unité de recherche de l'institut du thorax

Motivation: Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard Linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries. Results: In this study, we developed a set of tools namely bioalcidae, samjs and vcffilterjs that reformat or filter files using a JavaScript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk). Availability and implementation: https://github.com/lindenb/jvarkit. Contact: [e-mail].

Domaines: Sciences du Vivant [q-bio]

Pierre Lindenbaum, Richard Redon. bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files. Bioinformatics, 2018, Equipe I, 34 (7), pp.1224--1225. ⟨10.1093/bioinformatics/btx734⟩. ⟨hal-01833317⟩