https://github.com/grailbio/bio

Bioinformatic infrastructure libraries
https://github.com/grailbio/bio

bioinformatics data-science golang

Last synced: about 22 hours ago
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Bioinformatic infrastructure libraries

• Host: GitHub
• URL: https://github.com/grailbio/bio
• Owner: grailbio
• License: apache-2.0
• Created: 2018-03-26T18:55:40.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2020-08-18T18:34:59.000Z (about 4 years ago)
• Last Synced: 2024-08-03T01:13:48.119Z (3 months ago)
• Topics: bioinformatics, data-science, golang
• Language: Go
• Homepage:
• Size: 1.18 MB
• Stars: 73
• Watchers: 18
• Forks: 16
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-bio-go - Grail Bioinformatics tools

README

        
## Bioinformatics tools

- [bio-fusion](https://github.com/grailbio/bio/tree/master/fusion): High-performance RNA/DNA fusion detector

## Infrastructure libraries

- [encoding/bamprovider](https://godoc.org/github.com/grailbio/bio/encoding/bamprovider): Parallel BAM/PAM reader and parallel paired reader.

- [encoding/fasta](https://godoc.org/github.com/grailbio/bio/encoding/fasta): FASTA reader and writer.

- [encoding/fastq](https://godoc.org/github.com/grailbio/bio/encoding/fastq): FASTQ reader

- [encoding/pam](https://godoc.org/github.com/grailbio/bio/encoding/pam): A faster, smaller alternative to BAM files.

- [encoding/bam](https://godoc.org/github.com/grailbio/bio/encoding/bam): Utilities for BAM files. Based on github.com/biogo/hts.

- [encoding/converter](https://godoc.org/github.com/grailbio/bio/encoding/converter): Conversion between file formats

- [cmd/bio-pamtool](https://github.com/grailbio/bio/tree/master/cmd/bio-pamtool): "samtool" like tool for PAM and BAM.

- [cmd/bio-bam-sort](https://github.com/grailbio/bio/tree/master/cmd/bio-bam-sort): Tool for sorting and merging aligner outputs into PAM or BAM.

- [cmd/bio-bam-gindex](https://github.com/grailbio/bio/tree/master/cmd/bio-bam-gindex): Alternate index for faster seeking into BAM files.

- [cmd/bio-pileup](https://github.com/grailbio/bio/tree/master/cmd/bio-pileup): Tool to support variant calling on PAM or BAM.

- [biosimd](https://godoc.org/github.com/grailbio/bio/biosimd): Fast reverse-complement, pack/unpack from BAM seq[] format, etc.