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Table 2 Stampy (version 1.0.22) parameters to simulate reads

From: MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

Genome Stampy parameters
E.coli (format genome) -G ecoli ecoli_K12_MG1665.fasta
(hash) -g ecoli -H ecoli
(simulate) -g ecoli -h ecoli -S SRR522163_1.fastq
Human (format genome) -G hs_ref_GRCh37.p13_chr1
  hs_ref_GRCh37.p13_chr1.fa
(hash) -g hs_ref_GRCh37.p13_chr1
  -H hs_ref_GRCh37.p13_chr1
(simulate) -g hs_ref_GRCh37.p13_chr1
  -h hs_ref_GRCh37.p13_chr1
  -S ERR315985_to_ERR315997_1.fastq
Divergence  
.1 –substitutionrate=.1
.2 –substitutionrate=.2
.3 –substitutionrate=.3
.1+gaps –substitutionrate=.1 –simulate-minindellen=-30
  –simulate-maxindellen=30 –insertsize=250
  –insertsd=25
.2+gaps –substitutionrate=.2 –simulate-minindellen=-30
  –simulate-maxindellen=30 –insertsize=250
  –insertsd=25
.3+gaps –substitutionrate=.3 –simulate-minindellen=-30
  –simulate-maxindellen=30 –insertsize=250
  –insertsd=25