Verticall repair

The verticall repair command is a simple tool to repair an assembly, making it suitable for use in verticall pairwise. Specifically, it removes any ambiguous bases, splitting contigs wherever they occur. The result is an assembly containing only A, C, G and T. You should only need to use this command if verticall pairwise refuses to accept an assembly as input.

Example usage

Repairing one assembly, saving to a new file:

verticall repair -i assembly.fasta -o assembly_fixed.fasta

Repairing one assembly, overwriting the original:

verticall repair -i assembly.fasta -o assembly.fasta

Repairing all assemblies in a directory, overwriting the original files:

for f in *.fasta; do
    verticall repair -i "$f" -o "$f"
done

If you have a lot of assemblies, you can run that loop in parallel:

N=16
(
for f in *.fasta; do
   ((i=i%N)); ((i++==0)) && wait
   verticall repair -i "$f" -o "$f" &
done
)

Full help output

usage: verticall repair -i IN_FILE -o OUT_FILE [-h] [--version]

repair assembly for use in Verticall

Required arguments:
  -i IN_FILE, --in_file IN_FILE    Filename of assembly in need of repair
  -o OUT_FILE, --out_file OUT_FILE
                                   Filename of repaired assembly output (if the same as -i, the input
                                   file will be overwritten)

Other:
  -h, --help                       Show this help message and exit
  --version                        Show program's version number and exit