Autocycler gfa2fasta - rrwick/Autocycler GitHub Wiki

Basics

Autocycler gfa2fasta is a simple utility for converting an Autocycler GFA file into FASTA format. It's typically run on the GFA files produced by Autocycler clean or Dnaapler. It is useful when you want a standard FASTA file for downstream tasks such as polishing, annotation or submission.

Each FASTA record corresponds to a segment in the input GFA. The sequence name will match the segment name (a tig number), and the header will also include the sequence length and circular=true if the sequence is circular.

Example FASTA header: >1 length=2885786 circular=true

Example command

autocycler gfa2fasta -i autocycler.gfa -o autocycler.fasta

Full usage

Usage: autocycler gfa2fasta --in_gfa <IN_GFA> --out_fasta <OUT_FASTA>

Options:
  -i, --in_gfa <IN_GFA>        Input Autocycler GFA file (required)
  -o, --out_fasta <OUT_FASTA>  Output FASTA file (required)
  -h, --help                   Print help
  -V, --version                Print version
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