Table 2.
Stampy (version 1.0.22) parameters to simulate reads
| 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 |