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Simulate your reads with pbsim3
By BioStar 3 hours ago
#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
