NAME

App::SimulateReads::Command::Simulate::Custom - simulate subcommand class. Simulate a custom sequencing

VERSION

version 0.11

DESCRIPTION

Simulate a custom sequencing.

SYNOPSIS simulate_reads simulate custom [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:"."]
  -j, --jobs               number of jobs [default:"1"; Integer]
  -z, --output-gzip        compress output file
  -c, --coverage           fastq-file coverage [default:"8", Number]
  -n, --number-of-reads    directly set the number of reads [Integer]
  -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 mean size fragments for paired-end reads
                           [default:"300"; Integer]
  -d, --fragment-stdd      the standard deviation for fragment sizes
                           [default:"50"; Integer]
  -b, --strand-bias        which strand to be used: plus, minus and random
                           [default:"random"]
  -w, --seqid-weight       seqid raffle type: length, same, file
                           [default: "length"]
  -f, --weight-file        an expression-matrix when seqid-weight=file

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

--jobs

Sets the number of child jobs to be created

--output-gzip

Compress the output-file with gzip algorithm. It is possible to pass --no-output-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

--number-of-reads

Sets directly the number of reads desired. It overrides coverage, in case the two options are given

--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

--strand-bias

Sets which strand to use to make a read. Valid options are plus, minus and random - if you want to randomly calculte the strand for each read

--seqid-weight

Sets the seqid (e.g. chromossome, ensembl id) raffle behavior. Valid options are length, same and file. If it is set to 'same', all seqid receives the same weight when raffling. If it is set to 'length', the seqid weight is calculated based on the seqid sequence length. And finally, if it is set to 'file', the user must set the option --weight-file. For details, see --weight-file

--weight-file

If --seqid-weight is set to file, then this option becomes mandatory. A valid weight file is an expression-matrix file with 2 columns. The first column is for the seqid and the second column is for the count. The counts will be treated as weights

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