PERsim (0.1-222-g9be2128)
Paired-end read simulator for Illumina reads.
PERsim generates paired-end reads of a given length for a region of interest in the genome:
- insert size is modelled using a gaussian distribution.
- read-through into the sequencing adapters is modelled.
- sequencing errors are modelled using a simple uniform distribution.
Mandatory parameters:
-roi <file> Target region BED file (the corresponding reference genome is taken from the settings.ini file).
-count <int> Number of read pairs to generate.
-out1 <file> Forward reads output file in .FASTQ.GZ format.
-out2 <file> Reverse reads output file in .FASTQ.GZ format.
Optional parameters:
-length <int> Read length for forward/reverse reads.
Default value: '100'
-ins_mean <int> Library insert size mean value.
Default value: '200'
-ins_stdev <int> Library insert size mean standard deviation.
Default value: '70'
-error <float> Base error probability (uniform distribution).
Default value: '0.01'
-max_n <int> Maximum number of N bases (from reference genome).
Default value: '5'
-a1 <string> Forward read sequencing adapter sequence (for read-through).
Default value: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTTA'
-a2 <string> Reverse read sequencing adapter sequence (for read-through).
Default value: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTC'
-ref <file> Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
Default value: ''
-v Enable verbose debug output.
Default value: 'false'
Special parameters:
--help Shows this help and exits.
--version Prints version and exits.
--changelog Prints changeloge and exits.
--tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.