Troubleshooting inaccurate scaffolds

[malonge]

If your scaffolds don't look right, I suggest using Nucmer instead of Minimap2. To do this, use the following parameters:

ragtag.py scaffold --aligner /path/to/nucmer --nucmer-params='--maxmatch -l 100 -c 500' ref.fa query.fa

I suggest reading the MUMmer docs to learn about the --maxmatch, -l and -c parameters. Depending on the assemblies, one may consider increasing the seed and cluster size values to save time and to improve specificity. Removing --maxmatch might also save time without sacrificing accuracy.

I plan to provide a more detailed wiki section on this topic in the future.