App::SimulateReads::Command::Genome - simulate command class. Simulate genome sequencing


version 0.16


 simulate_reads genome [options] <fasta-file>

  a fasta-file 

  -h, --help                     brief help message
  -M, --man                      full documentation
  -v, --verbose                  print log messages
  -p, --prefix                   prefix output [default:"out"]  
  -o, --output-dir               output directory [default:"."]
  -i, --append-id                append to the defined template id [Format]
  -I, --id                       overlap the default template id [Format]
  -j, --jobs                     number of jobs [default:"1"; Integer]
  -z, --gzip                     compress output file
  -s, --seed                     set the seed of the base generator
                                 [default:"time()"; Integer]
  -c, --coverage                 fastq-file coverage [default:"8", Number]
  -t, --sequencing-type          single-end or paired-end reads
  -q, --quality-profile          illumina sequencing system profiles
  -e, --sequencing-error         sequencing error rate
                                 [default:"0.005"; Number]
  -r, --read-size                the read size [default:"100"; Integer]
                                 the quality_profile from database overrides
                                 this value
  -m, --fragment-mean            the fragment mean size for paired-end reads
                                 [default:"300"; Integer]
  -d, --fragment-stdd            the fragment standard deviation size for
                                 paired-end reads [default:"50"; Integer]


Simulate genome sequencing.



Print a brief help message and exits.


Prints the manual page and exits.


Prints log information to standard error


Concatenates the prefix to the output-file name.


Creates output-file inside output-dir. If output-dir does not exist, it is created recursively


Append string template to the defined template id. See Format


Overlap the default defined template id: single-end %i.%U_%c_%s_%t_%n and paired-end %i.%U_%c_%s_%S_%E e.g. SR123.1_chr1_P_1001_1101 See Format


A string Format is a combination of literal and escape characters similar to the way printf works. That way, the user has the freedom to customize the fastq sequence identifier to fit her needs. Valid escape characteres are:

Common escape characters

        Escape       Meaning
        ------       ------------------------------------------
        %i           instrument id composed by SR + PID
        %I           job slot number
        %q           quality profile
        %e           sequencing error
        %R           read 1, or 2 if it is the paired-end mate
        %U           read number
        %r           read size
        %c           sequence id as chromossome, ref
        %s           read or fragment strand
        %t           read start position
        %n           read end position

Paired-end specific escape characters

        Escape       Meaning
        ------       ------------------------------------------
        %T           mate read start position
        %N           mate read end position
        %D           distance between the paired-reads
        %m           fragment mean
        %d           fragment standard deviation
        %f           fragment size
        %S           fragment start position
        %E           fragment end position

Sets the number of child jobs to be created


Compress the output-file with gzip algorithm. It is possible to pass --no-gzip if one wants uncompressed output-file


Sets the seed of the base generator. The ability to set the seed is useful for those who want reproducible simulations. Pay attention to the number of jobs (--jobs) set, because each job receives a different seed calculated from the main seed. So, for reproducibility, the same seed set before needs the same number of jobs set before as well.


Sets the read size, if quality-profile is equal to 'poisson'. The quality-profile from database overrides the read-size


Calculates the number of reads based on the sequence coverage: number_of_reads = (sequence_size * coverage) / read_size. This is the default option for genome sequencing simulation


Sets the sequencing type to single-end or paired-end


If the sequencing-type is set to paired-end, it sets the fragment mean


If the sequencing-type is set to paired-end, it sets the fragment standard deviation


Sets the sequencing error rate. Valid values are between zero and one


Sets the illumina sequencing system profile for quality. For now, the unique valid values are hiseq and poisson


Thiago L. A. Miller <>


This software is Copyright (c) 2018 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007