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Table of Simulation Parameters
Moritz Smolka edited this page Jul 21, 2017
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This page contains a list of parameters for creating data sets using the internal Teaser simulation pipeline.
| Parameter | Default | Description |
|---|---|---|
| reference | (None) | Path relative to Teaser/references directory for mapping reference FASTA file |
| platform | illumina | Sequencing platform. Can be illumina, 454 or ion_torrent |
| read_length | 100 | Average Read length to simulate |
| read_count | (Calculated) | Calculated based on subsampling parameters. Must be set manually if subsampling is disabled. |
| coverage | 1 | Multiplier for read count |
| paired | No | Library is paired-end? |
| insert_size | 500 | Inner distance in base pairs between the outer ends of both reads in a pair |
| insert_size_error | 50 | Standard deviation for insert size |
| mutation_rate | 0.001 | Overall rate of mutations (0-1) |
| mutation_indel_frac | 0.3 | Fraction of overall mutations that are indels - the rest are SNPs. |
| mutation_indel_avg_len | 1 | Average length for indels in base pairs |
| error_rate_mult | 1 | Multiplier for overall sequencing error rate |
Prior to simulation, Teaser by default samples a number of small regions from the reference genome. For most use cases it is sufficient to rely on the default values for this process.
| Parameter | Default | Description |
|---|---|---|
| enable | Yes | Should the reference genome be subsampled for simulation |
| ratio | (Calculated) | Fraction of the original reference to sample |
| region_len_multiplier | 10 | Region length is calculated by multiplying this value with the read length / insert size |
| region_pad | (Calculated) | Padding to add between subsampled regions (defaults to 2 x read length / insert size) |
| region_len | (Calculated) | Set to manually override the subsampling region length |