Echidna_sexchromosome

This repository include three piplines used in echidna genome study, mainly about the sex chromosome analysis.

X/Y identity & strata divergence calculation

This pipline (in XY_identity) include two steps:

1. Calculate X/Y identity based on lastZ MAF and NET results.
2. Calculate strata divergence by baseml with MAF.

Hi-C Strength comparison

This pipline (in HiC_strength_compared) is used to confirm if an unplaced scaffold is autosomal or sex-linked, by comparing Hi-C strength between the scaffold with assigned chromosomes.

Ampliconic region annotation

This pipeline (in Ampliconic_Annotation) includes five steps:

1. Repeat annotation with TRF, RepeatMasker & RepeatModeler
2. Palindrome detection with lastz and palindrover
3. Tandem ampliconic region identified with blastn
4. Collapsed ampliconic region identified with male sequencing depth
5. Combine the ampliconic regions above.