merge

Detailed documentation coming soon!

Merging and reconciling scaffolds

positional arguments:
  <asm.fasta>           assembly fasta file (uncompressed or bgzipped)
  <scf1.agp> <scf2.agp> [...]
                        scaffolding AGP files

optional arguments:
  -h, --help            show this help message and exit

merging options:
  -f FILE               CSV list of (AGP file,weight) [null]
  -j <skip.txt>         list of query headers to leave unplaced [null]
  -l INT                minimum assembly sequence length [100000]
  -e FLOAT              minimum edge weight. NA if using Hi-C [0.0]
  --gap-func STR        function for merging gap lengths {'min', 'max', or 'mean'} [min]

input/output options:
  -o PATH               output directory [./ragtag_output]
  -w                    overwrite intermediate files
  -u                    add suffix to unplaced sequence headers

Hi-C options:
  -b FILE               Hi-C alignments in BAM format, sorted by read name [null]
  -r STR                CSV list of restriction enzymes/sites or 'DNase' [GATC]
  -p FLOAT              portion of the sequence termini to consider for links [1.0]
  --list-enzymes        list all available restriction enzymes/sites