conf_for_big_genome.txt

[hisat2]
--min-intronlen 20 --max-intronlen 50000 --dta --score-min L,0.0,-0.4

[geneModels2AugusutsTrainingInput]
--min_evalue 1e-9 --min_identity 0.8 --min_coverage_ratio 0.8 --min_cds_num 2 --min_cds_length 600 --min_cds_exon_ratio 0.60

[paraCombineGeneModels]
--overlap 30 --min_augustus_transcriptSupport_percentage 50.0 --min_augustus_intronSupport_number 1 --min_augustus_intronSupport_ratio 0.5 --more_strict

[GFF3_extract_TranscriptID_for_filtering]
--min_CDS_ratio 0.5 --min_CDS_length 750 --max_repeat_overlap_ratio 0.2 --ignore_repeat_Name Simple_repeat,Low_complexity,Satellite,Unknown,Tandem_repeat

[para_hmmscan]
--evalue1 1e-10 --evalue2 1e-6 --hmm_length 80 --coverage 0.5 --no_cut_ga --chunk 20 --hmmscan_cpu 2

[parsing_blast_result.pl]
--evalue 1e-10 --identity 0.1 --CIP 0.5 --subject-coverage 0.5 --query-coverage 0.5

[get_valid_transcriptID]
--hmm_evalue 1e-20 --hmm_coverage 0.8 --blast_evalue 1e-20 --blast_CIP 0.8 --blast_coverage 0.8 --blast_evalue_for_genesie 1e-10 --blast_CIP_for_genewise 0.8 --blast_coverage_for_genewise 0.9
# add --both_required for more strcit.

[get_valid_geneModels]
--discard_Filling2Uncomplete