bio 0.0.5

Some useful command line utils written in Dart. For parsing and manipulating sequence records in various formats...

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

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• 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