reassign-sex-chr

This pipeline was first designed by @projectoriented

Methodology

All contigs which align to the sex chromosomes are assigned into hap1 (chrY) and hap2 (chrX) based on alignments to a reference

1. Alignments are made to a given reference with chrX and chrY (in most cases CHM13)
2. Contigs are sorted into one of two categories:
   • Complement (Split)
     • Those contigs which do not have an overlap with another contig in the opposite haplotype but are located in the haplotype not designated to that sex chromosome
   • Align (Duplicated)
     • Those contigs which have overlapping alignments with contigs in another haplotype for the same chromosome and coordinates
   • By default these criteria are required to reach a 95% reciprocal overlap to determine similarity
3. The pipeline can either produce just a list of contigs and their desired assignments, or reorder the input fasta files accordingly

Running the pipeline

Step 1. Prepare directory

config
├── config.yaml
└── manifest.tab
runsnake

Step 2. Prepare inputs

config/config.yaml

reference: /net/eichler/vol26/eee_shared/assemblies/CHM13/T2T/v2.0/T2T-CHM13v2.fasta

#### OPTIONAL ARGS
minimap_params: '-x asm20 --secondary=no -s 25000'
manifest: config/manifest.tab

config/manifest.tab

sample  hap1    hap2
your_sample path/to/hap1_asm    /path/to/hap2_asm

Step 3. Start the analysis!

ln -s /net/eichler/vol27/projects/autism_genome_assembly/nobackups/scratch/wumei/fix_sex_chr/runsnake .
./runsnake 30