Error_rates_in_Herro_and_corrected_Herro_reads_compared_to_NextSeq2000

README.txt

# output from best commit #fcdfa97 (https://github.com/google/best), .summary_identity_stats.csv files using reads
# aligned to concatenated chr20_MATERNAL and chr20_PATERNAL from hg002v1.0.1.fasta.gz (https://github.com/marbl/HG002) (https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.0.1.fasta.gz)
# using mm2-fast commit # 10bde16 using settings: --eqx --secondary=no -Y -c -ax map-ont -k 19 -w 13 -t 48 
# or using these settings for Illumina NextSeq2000 reads: -t 48 --eqx --secondary=no -acx sr
#
# brutal_rewrite (br) commit # ad87f92 (https://github.com/natir/br) using settings: -k 19 -m graph
# kmer read filter (kmrf) commit # 36cad24 (https://github.com/natir/kmrf) using setting: -k 17
# peregrine-2021 (pg_asm) commit # 6698eb1 (https://github.com/cschin/peregrine-2021): using default settings
#
# herro (herro) commit # c41dc30 (https://github.com/lbcb-sci/herro) using defaults and model at time of commit
#
total_alns  primary_alns  identity  identity_qv  gap_compressed_identity  matches_per_kbp  mismatches_per_kbp  non_hp_ins_per_kbp  non_hp_del_per_kbp  hp_ins_per_kbp  hp_del_per_kbp data
65619       63818         0.999095  30.434695    0.999463                 999.346981       0.208796            0.166975            0.135951            0.084988        0.308272       herro (SUP reads with Dorado 0.5.0 and dna_r10.4.1_e8.2_400bps_fast@v4.3.0 corrected with herro)
65699       63818         0.999259  31.302137    0.999606                 999.485771       0.155193            0.155439            0.099600            0.071445        0.259436       herro_br (herro reads corrected with br)
64740       63784         0.999268  31.352016    0.999610                 999.492636       0.152168            0.154074            0.097595            0.071211        0.257602       herro_br_kmrf (herro reads corrected with br then filtered with kmrf)
63181       62861         0.999449  32.587523    0.999717                 999.624137       0.111094            0.123707            0.062817            0.051649        0.201953       herro_br_kmrf_pg_asm1x (herro reads corrected with br then filtered with kmrf then corrected with one round of pg_asm)
63069       62788         0.999480  32.840919    0.999737                 999.647928       0.102495            0.119696            0.056975            0.048205        0.192603       herro_br_kmrf_pg_asm2x (herro reads corrected with br then filtered with kmrf then corrected with two rounds of pg_asm)
63055       62773         0.999479  32.830965    0.999737                 999.646587       0.103096            0.119842            0.057305            0.047912        0.193012       herro_br_kmrf_pg_asm3x (herro reads corrected with br then filtered with kmrf then corrected with three rounds of pg_asm)
63068       62788         0.999480  32.838353    0.999737                 999.647803       0.102685            0.119890            0.056948            0.048194        0.192564       herro_br_kmrf_pg_asm2x_br (herro reads corrected with br then filtered with kmrf then corrected with two rounds of pg_asm then corrected with br again)
2591984     2579459       0.995597  23.562761    0.995737                 995.677787       4.145387            0.048807            0.065647            0.032084        0.111180       Illumina_NextSeq2000_exome_sequencing_150bp_paired-end_raw_reads