The usage and help documentation of can be seen by running -h:

usage: - [-h] [-c CHUNK_SIZE] [-o OVERLAP_SIZE] [-m] [-b BEDFILE]
         contigs [contigs ...]

Cut up fasta file in non-overlapping or overlapping parts of equal length.

Optionally creates a BED-file where the cutup contigs are specified in terms
of the original contigs. This can be used as input to

positional arguments:
  contigs               Fasta files with contigs

optional arguments:
  -h, --help            show this help message and exit
  -c CHUNK_SIZE, --chunk_size CHUNK_SIZE
                        Chunk size
  -o OVERLAP_SIZE, --overlap_size OVERLAP_SIZE
                        Overlap size
  -m, --merge_last      Concatenate final part to last contig
  -b BEDFILE, --bedfile BEDFILE
                        BEDfile to be created with exact regions of the
                        original contigs corresponding to the newly created


An example of how to run original_contigs.fa -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa

This creates a fasta file and a BED file. The fasta file contigs_10K.fa contains the original contigs cut up into parts of length exactly 10K, except for the last contig part which is between 10K and 20K long. The BED file contigs_10K.bed contains a list of the contig parts created with coordinates in the original contigs.