logsdon-lab / CenMAP

Centromere mapping and annotation pipeline

MIT License

9 stars 0 forks source link

readme

`CenMAP`

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

HGSVC3 chr1 centromere HOR structure, centromere dip regions, and self-identity plot.

HGSVC3 chr12 centromere HOR structure.

HGSVC3 Cumulative alpha-satellite HOR array lengths by chromosome.

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.
Centromere alpha-satellite higher order repeat (HOR) array lengths.
RepeatMasker and HumAS-HMMER alpha-satellite HOR monomer annotations and plots.
ModDotPlot sequence identity plots.
Combined sequence identity and HOR array structure plots.
(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.