bio

Functions and command line tools for biological computation written in Dart.

CI Status Release Publish Pub Version

USAGE

  • As a dart package

    • Add bio in pubspec.yaml
    • Run pub get
  • As a command line tool

    • Download binary from release. linux, mac and win are available.
    • Extract the binary file 7z e bio-xxx.7z
    • Run ./bio + subcommand

DOCUMENTATION

eg, convert fastq into fasta, then subsamples 2 records and reverse complement the sequences.

bio seq --input ./data/seq.fq \
        --output ./data/seq_sampled.fa \
        --sample 2 --sample-seed 123 \
        --reverse-complement

BENCHMARK

tooltest IO timetest RC time
biodart6.67815.533
seqkit (Golang)0.9960.879
seqtk (C)0.8490.854

Libraries

bio
phylo
popgen
seq
tree
utils