CenMAP

A centromere mapping and annotation pipeline for T2T human genome assemblies implemented in Snakemake.

Chr1 α-satellite higher-order repeat structure, centromere dip regions, and self-identity plot	Chr12 α-satellite HOR arrays
Cumulative α-satellite HOR array lengths

Input

• Verkko or hifiasm human genome assemblies
• PacBio HiFi reads used in the assemblies
• CHM13 reference genome assembly
• (Optional) Unaligned BAM files with 5mC modifications at CpG sites.

Output

• Complete and correctly assembled centromere sequences and their regions validated by NucFlag.
• Centromere alpha-satellite higher order repeat (HOR) array lengths via censtats.
• RepeatMasker and HumAS-SD alpha-satellite HOR monomer annotations and plots.
• ModDotPlot sequence identity plots.
• Combined sequence identity and HOR array structure plots via cenplot.
• (Optional) Centromere dip region (CDRs) with CDR-Finder

Documentation

Read the docs on the CenMAP wiki.

Tests

To run tests, refer to the wiki page.