Autocycler gfa2fasta - rrwick/Autocycler GitHub Wiki

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 depth. If the sequence is a circular and complete component of the graph, it will contain circular=true topology=circular in its header. If it is a linear and complete component of the graph, it will contain circular=false topology=linear. If it is incomplete (i.e. part of a multi-tig component), it will not contain circular or topology. See Metrics for more information on topology.

Example FASTA header: >1 length=2885786 depth=8.0 circular=true topology=circular

The depth comes from the input GFA's DP tag, so its meaning depends on which graph you convert. For most Autocycler graphs it is the number of times the sequence occurs in the input contigs, but for a consensus_assembly.gfa made by Autocycler combine with reads, it is the read depth.

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

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

• A GFA cannot mark a sequence as having no read depth (see Autocycler combine), so such sequences will get depth=0.0 here, whereas the FASTA made by Autocycler combine gives them depth=unavailable. This is only likely to affect sequences which consist entirely of repeat sequences.