NAME
App::SimulateReads::Command::Digest - digest command class. Simulate single-end and paired-end reads.
VERSION
version 0.08
SYNOPSIS
simulate_reads digest [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, --gzip compress output file
-c, --coverage fastq-file coverage [default:"1", Number]
-n, --number-of-reads directly set the number of reads
[default:"1", 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 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]
-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 weight file when seqid-weight=file
DESCRIPTION
simulate_reads will read the given input file and do something useful with the contents thereof.
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
- --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
- --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 a tab-separated values file with 2 columns. The first column is for the seqid and the second column for the desired weight. Valid weights are integers
AUTHOR
Thiago L. A. Miller <tmiller@mochsl.org.br>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2017 by Teaching and Research Institute from Sírio-Libanês Hospital.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007