y9c / biodart

🔬 A dart package for bioinformatics

bio

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

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

• Read the CMD documentation to find out more examples:

  https://biodart.yech.xyz

• Read the API documentation to find out more details:

  https://pub.dev/documentation/bio

BENCHMARK

tool	test IO time	test RC time
biodart	6.678	15.533
seqkit (Golang)	0.996	0.879
seqtk (C)	0.849	0.854