App::SimulateReads::Command::Simulate::Custom - simulate subcommand class. Simulate a custom sequencing
version 0.14
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:"."] -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] -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
Simulate a custom 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 %U and paired-end %i.%U %U e.g. SR123.1 1 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-output-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. 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 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
Thiago L. A. Miller <tmiller@mochsl.org.br>
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
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.