Nextomics
using Nextpolish and after polished ,produce more contigs
Hi i used Nextpolish to polish my primary contigs fasta finished by Canu2.0. I followed the tutoral——using PE-short reads and Pacbio long reads for two rounds each. here is my code: ######################################################## job_type = local job_prefix = nextPolish task = best rewrite = yes rerun = 3 parallel_jobs = 8 multithread_jobs = 8 genome =genome.contigs.fasta genome_size = auto workdir = ./01_rundir polish_options = -p 8
[sgs_option] sgs_fofn = ./sgs.fofn sgs_options = -max_depth 100
[lgs_option]
lgs_fofn = ./lgs.fofn
lgs_options = -min_read_len 10k -max_read_len 150k -max_depth 60
lgs_minimap2_options = -x map-ont -t 8
########################################################
but after i polished my genome contigs ,i found that the contigs numbers increased highly,following figures are my genome.contigs.fasta、genome.nextpolish.contigs.fasta consequences statistics
could you tell me how to deal with it?
what is the version of NextPolish you are using? Could you paste some seq IDs in the polished genome while not existed in the original genome?
