App::SimulateReads::Command::Digest - digest command class. Simulate single-end and paired-end reads.
version 0.10
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
simulate_reads will read the given input file and do something useful with the contents thereof.
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
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 read size. For now the unique valid value is 101
Calculates the number of reads based on the sequence coverage: number_of_reads = (sequence_size * coverage) / read_size
Sets directly the number of reads desired. It overrides coverage, in case the two options are given
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
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
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
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
Thiago L. A. Miller <tmiller@mochsl.org.br>
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
To install App::SimulateReads, copy and paste the appropriate command in to your terminal.
cpanm
cpanm App::SimulateReads
CPAN shell
perl -MCPAN -e shell install App::SimulateReads
For more information on module installation, please visit the detailed CPAN module installation guide.