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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