https://bioinformaticsonline.com/snippets/view/45461/simulate-your-reads-with-pbsim3? https://bioinformaticsonline.com/snippets/view/45461/simulate-your-reads-with-pbsim3 Wed, 04 Nov 2026 04:03:36 -0600 https://bioinformaticsonline.com/snippets/view/45461/simulate-your-reads-with-pbsim3 #Install it using conda conda install bioconda::pbsim3 (sutraENV) bio@Biostar-Latitude-7490:~/Downloads/SUTRA-v0.9.24-native$ pbsim --strategy wgs --method qshmm --qshmm data/pbsim3/data/QSHMM-ONT-HQ.model --depth 500 --genome data/both.fa :::: Simulation parameters ::: strategy : wgs method : qshmm qshmm : data/pbsim3/data/QSHMM-ONT-HQ.model genome : data/both.fa prefix : sd id-prefix : S depth : 500.000000 length-mean : 9000.000000 length-sd : 7000.000000 length-min : 100 length-max : 1000000 difference-ratio : 6:55:39 seed : 1793785971 accuracy-mean : 0.850000 pass_num : 1 hp-del-bias : 1.000000 :::: Reference stats :::: file name : data/both.fa ref.1 (len:48576) : gi|9626243|ref|NC_001416.1| Enterobacteria phage lambda, complete genome ref.2 (len:48576) : mutated_1000 :::: Simulation stats (ref.1) :::: read num. : 2632 depth : 500.000062 read length mean (SD) : 9227.964666 (7156.710332) read length min : 159 read length max : 50386 read accuracy mean (SD) : 0.849734 (0.046237) substitution rate. : 0.008996 insertion rate. : 0.082538 deletion rate. : 0.058546 :::: Simulation stats (ref.2) :::: read num. : 2672 depth : 500.001173 read length mean (SD) : 9089.841692 (7097.508269) read length min : 112 read length max : 49709 read accuracy mean (SD) : 0.851198 (0.046289) substitution rate. : 0.008973 insertion rate. : 0.082194 deletion rate. : 0.058268 :::: System utilization :::: CPU time(s) : 5 Elapsed time(s) : 31]]> BioStar