Since many downstream analyses will be performed relative to 38, can you think about (and decide) how to handle this sequence:

chrY_KI270740v1_random (37240 bp)

run with default parameters

identify clusters of HET variants as potential misassembled regions

Pille updated seq. class definitions in google doc

Export to BED and rerun modules 20 and 60

@ptrebert
Do you think it would help to open a project here - I can try to start writing things down step-by-step.

Add the following motifs to HMMER runs (various purposes)
FASTA files located under references

• DYZ19_Yq: located in Yq euchromatin, not for contig identification, just annotate chrY contigs
• DYZ3-prim_Ycentro: 171bp rep unit, not for contig identification, just annotate chrY contigs
• DYZ3-sec_Ycentro: 5941bp rep unit, threshold hits >1700 and use for contig identification
• "TSPY": to be defined

Pille:

Additional Y sequence annotations from hg38 - please add a step to align these to all chrY assemblies:
- using '--secondary=no'
- using '--secondary=yes' but not restricting the number of sec.alignments allowed
I've added both the bed and fasta to Globus /HHU/references/ - GRCh38_chrY-seq-classes_coord_plus_repeats.bed/fasta
These contain most of the Y repeats and SDs, so they are useful to understand the Y structure.

Primary interest: HiFi reads

Requested output by Pille:

read depth, both with and without secondary alignments

@ptrebert
Btw, were you serious about a one-liner for comparing 2 fasta sequences? Can you write this (can be multiple lines as well :P) in like few minutes?
It would be even better if it could take as input multiple fasta sequences (an alignment essentially) and then output the site across all sequences + position in the sequence in case there is a difference between the sequences. Maybe in a similar format to vcf - one site per row: position, gt/sample1, gr/sample1 etc. I can kind of think of a way of writing it but in reality it would take me more time than I would like.

Order (orient) identified chrY contigs on the basis of the contig-to-reference alignments relative to T2T.
Contigs should be renamed; coordinate with Pille about naming convention.

Pille:

Contig names - maybe something as easy as just numbering from PAR1 as 1 to PAR2. E.g. chrY_01 to chrY_N?
Or do you think it would be worth retaining the original contig names as well?
[...] does it make sense to keep those with original contig names, or do we just rename the Y contigs?

implement a simple strategy (i.e. rule-based) to identify chrY contigs in the de novo assemblies.

Current rule set:

• 1. tig has only chrY alignments
• 2. tig has mixed alignments but Y-specific motif hits (above threshold)
• 3. tig has primary alignments to chrY with many (current T: >300) unspecific motif hits (above threshold)
• 4. tig is unaligned and has Y-specific motif hits (above threshold)
• 5. tig has more than 90% bp primary alignments to chrY

Motif hits above threshold = "high-quality hits", thresholds set by expert curation