NAME

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

VERSION

version 0.12

SYNOPSIS

 simulate_reads simulate genome [options] <fasta-file>

 Arguments:
  a fasta-file 

 Options:
  -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
  -c, --coverage           fastq-file coverage [default:"8", Number]
  -t, --sequencing-type    single-end or paired-end reads
                           [default:"paired-end"]
  -q, --quality-profile    illumina sequencing system profiles
                           [default:"hiseq"]
  -e, --sequencing-error   sequencing error rate
                           [default:"0.005"; Number]
  -r, --read-size          the read size [default:"101"; Integer]
  -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]

DESCRIPTION

Simulate genome sequencing.

OPTIONS

--help

Print a brief help message and exits.

--man

Prints the manual page and exits.

--verbose

Prints log information to standard error

--prefix

Concatenates the prefix to the output-file name.

--output-dir

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

--append-id

Append string template to the defined template id. See Format

--id

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

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

--jobs

Sets the number of child jobs to be created

--gzip

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

--read-size

Sets the read size. For now the unique valid value is 101

--coverage

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

--sequencing-type

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

--fragment-mean

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

--fragment-stdd

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

--sequencing-error

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

--quality-profile

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

AUTHOR

Thiago L. A. Miller <tmiller@mochsl.org.br>

COPYRIGHT AND LICENSE

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