Autocycler combine

Basics

This is the final step in an Autocycler assembly, where the resolved sequences for each cluster are combined into a single assembly.

Example command

autocycler combine -a autocycler_out -i autocycler_out/clustering/qc_pass/cluster_*/5_final.gfa

This command takes an Autocycler directory and one or more cluster graphs (typically 5_final.gfa). It will create consensus_assembly.fasta and consensus_assembly.gfa files in the Autocycler directory.

Full usage

Usage: autocycler combine --autocycler_dir <AUTOCYCLER_DIR> --in_gfas <IN_GFAS>...

Options:
  -a, --autocycler_dir <AUTOCYCLER_DIR>  Autocycler directory (required)
  -i, --in_gfas <IN_GFAS>...             Autocycler cluster GFA files (one or more required)
  -h, --help                             Print help
  -V, --version                          Print version

Notes

• While Autocycler combine is typically run using each cluster's final graph (5_final.gfa), it can also be run on earlier graphs (e.g. 4_merged.gfa) if desired.

Toy example

(The toy example is introduced on the Autocycler compress page.)

Since both of the clusters in the toy example were successfully resolved into a single circular consentig, Autocycler combine simply creates a single assembly with both of these consentigs.