README

Distortopia: simulation of long-read sequences, high-resolution mapping of meiotic crossovers, and identification of segregation distorters in Arabidopsis.

download Athaliana and Alyrata genomes from JGI Phytozome

$ curl --cookie jgi_session=/api/sessions/e68504ec0dc38906b76d27c0e311eeea --output download.20250726.142947.zip -d "{"ids":{"Phytozome-384":{"file_ids":["585486967ded5e78cff8c52c"],"top_hit":"683db57de69ed9082626f62f"},"Phytozome-447":{"file_ids":["587b0adf7ded5e4229d885ab"],"top_hit":"683db58de69ed9082626f687"}},"api_version":"2"}" -H "Content-Type: application/json" https://files-download.jgi.doe.gov/filedownload/

generate alt ref haploid genomes

$ python sim_haplotypes.py data/Ath 0.001 123 hap11 > data/ref1_hap1.fa $ python sim_haplotypes.py data/Ath 0.001 321 hap12 > data/ref1_hap2.fa $ python sim_haplotypes.py data/Aly 0.001 666 hap21 > data/ref2_hap1.fa $ python sim_haplotypes.py data/Aly 0.001 999 hap22 > data/ref2_hap2.fa

create alignments of each genome [minimap2 [options] target query]

$ minimap2 -x asm5 -t 6 data/ref1_hap2.fa data/ref1_hap1.fa > data/ref11xref12.paf

generate long reads from gametes of an artificial hybrid with uniform recomb

$ sim_gamete_pool_long_reads ref1_hap1.fa ref1_hap2.fa 100_000 1e6 > ref1xref1_gametes_longreads.fq.gz $ sim_gamete_pool_long_reads ref1_hap1.fa ref1_hap2.fa 100_000 1e6 > ref1xref2_gametes_longreads.fq.gz

map reads to the reference

$ align_gamete_longreads REF1 ref1xref1_gamete_longreads.fq.gz > ref1xref1_gametes.bam $ align_gamete_longreads REF1 ref1xref2_gamete_longreads.fq.gz > ref1xref2_gametes.bam

call variants

$ gamete_variant_calling ref1xref1_gametes.bam > ref1xref1_gametes.vcf $ gamete_variant_calling ref1xref1_gametes.bam > ref1xref2_gametes.vcf

run crossover detection

$ colmapper REF1 ref1xref1_gametes.vcf > ref1xref1_gametes_crossovers.tsv $ colmapper REF1 ref1xref2_gametes.vcf > ref1xref2_gametes_crossovers.tsv