README.md

ASMAPP

A workflow for appraising genome assemblies.

This workflow includes full assembly appraisal with the following methods:

-Read mapping with minimap2
-Assembly appraisal statistics with QUAST
-Mitochondrial contig flagging/removal
-Contaminant identification with Blobtools
-Variant calling with Sniffles
-Mapping stat generation
-Ploidy estimations with Genomescope and Smudgeplot
-Coverage analytics
-Homoeologous contig detection*
-Statistics on homoeolog differences*

See the docs for more details.