p_utg difference for inbreeding lines

[baozg]

Hi, @chhylp123

I am tring to assembly inbreeding accessions from A.thaliana. However, we noticed serveral ~1Mb scale heterzygous blocks in the genome. But it cannot find by the default parameters. How do this influence the p_utg?

same bin file

# default
~/software/hifiasm/0.23.0/hifiasm -t 32 demux_CCS.fastq -o Ath1_hifiasm.asm

Reads has been loaded.
Loading ma_hit_ts from disk...
ma_hit_ts has been read.
Loading ma_hit_ts from disk...
ma_hit_ts has been read.
[M::ha_assemble::14.333*0.89] ==> loaded corrected reads and overlaps from disk
[M::ha_opt_update_cov_min] updated max_n_chain to 300
[M::purge_dups] homozygous read coverage threshold: 120
[M::purge_dups] purge duplication coverage threshold: 150
[M::ug_ext_gfa::] # tips::65
Writing raw unitig GFA to disk...
Writing processed unitig GFA to disk...
[M::purge_dups] homozygous read coverage threshold: 120
[M::purge_dups] purge duplication coverage threshold: 150
[M::mc_solve:: # edges: 188]
[M::mc_solve_core_adv::0.017] ==> Partition
[M::adjust_utg_by_primary] primary contig coverage range: [102, infinity]
Writing PA2338_hifiasm.asm.bp.p_ctg.gfa to disk...
[M::reduce_hamming_error_adv::0.011] # inserted edges: 0, # fixed bubbles: 0
[M::adjust_utg_by_trio] primary contig coverage range: [102, infinity]
[M::recall_arcs] # transitive arcs::38
[M::recall_arcs] # new arcs::1264, # old arcs::806
[M::clean_trio_untig_graph] # adjusted arcs::0
[M::adjust_utg_by_trio] primary contig coverage range: [102, infinity]
[M::recall_arcs] # transitive arcs::74
[M::recall_arcs] # new arcs::1292, # old arcs::816
[M::clean_trio_untig_graph] # adjusted arcs::0
[M::output_trio_graph_joint] dedup_base::18637131, miss_base::0


# inbreeding 
~/software/hifiasm/0.23.0/hifiasm -t 32 demux_CCS.fastq -o Ath1_hifiasm.asm -l 0 --primary
Reads has been loaded.
Loading ma_hit_ts from disk...
ma_hit_ts has been read.
Loading ma_hit_ts from disk...
ma_hit_ts has been read.
[M::ha_assemble::11.573*1.00] ==> loaded corrected reads and overlaps from disk
[M::ha_opt_update_cov_min] updated max_n_chain to 300
[M::purge_dups] homozygous read coverage threshold: 60
[M::purge_dups] purge duplication coverage threshold: 75
[M::ug_ext_gfa::] # tips::65
Writing raw unitig GFA to disk...
Writing processed unitig GFA to disk...
[M::adjust_utg_by_primary] primary contig coverage range: [51, infinity]
Writing primary contig GFA to disk...
Writing alternate contig GFA to disk...

gfatoools stat of two gfa

# default bp.p_utg.gfa
Number of segments: 761
Number of links: 505
Number of arcs: 1010
Max rank: 0
Total segment length: 169151292
Average segment length: 222275.022
Sum of rank-0 segment lengths: 0
Max degree: 4
Average degree: 0.664

# -l 0 

Number of segments: 1061
Number of links: 939
Number of arcs: 1878
Max rank: 0
Total segment length: 180108688
Average segment length: 169753.712
Sum of rank-0 segment lengths: 0
Max degree: 4
Average degree: 0.885