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========================
Copyright: (c) 2010 by Manuel Holtgrewe
License: GPL v3.0
Homepage: http://www.seqan.de/projects/mason.html
Mason is a read simulator for second-generation sequencing data. At
the moment, the simulation of Illumina, 454 and Sanger reads is
supported.
How It Works
------------
Reads are sampled from a reference sequence. The reference sequence
is either read from a FASTA file or generated randomly given a
background distribution for nucleotides.
Then, modified copies of the reference sequence are generated to
simulate haplotypes.
Reads are then uniformly sampled from these haplotypes and sequencing
technology specific errors are introduced.
How To Call Mason
-----------------
The first argument specifies the sequencing technology to use. To get
a full list of options, use the argument --help.
mason illumina [OPTIONS] SEQUENCE --help
mason 454 [OPTIONS] SEQUENCE --help
mason sanger [OPTIONS] SEQUENCE --help
Important Global Options
------------------------
-s --seed NUM The seed for the random number generator. Use this
to simulate multiple different read sets with
otherwise identical parameters or in parallel.
-N --num-reads NUM Number of reads to generate.
-sq --simulate-qualities If given, qualities are simulated for the reads and
the result is a FASTQ file, is FASTA otherwise.
-o --output-file FILE Path to the resulting FASTA/FASTQ file.
Important Illumina Options
--------------------------
-n --read-length NUM Length of the reads to simulate.
Important Sanger/454 Options
----------------------------
-nm --read-length-mean Mean length of the reads to simulate.
-ne --read-length-error Error of the read length to simulate. If normal
distribution is used for read lengths (also see
--read-length-uniform), this is the standard
deviation.
Examples
--------
Simulate 100'000 Illumina mate-pairs with qualities from drosophila
genome without qualities to file myreads_1.fasta and myreads_2.fasta.
mason illumina -n 100000 -mp -o myreads.fasta drosophila.genom
Simulate 1'000 454 reads from diploid data with qualities to
myreads.fastq:
mason 454 -n 1000 -sq -hn 2 -o myreads.fastq drosophila.genom
Simulate 1'000 Illumina reads with qualities and error profile file
from errors.txt, scaled by 0.5 to myreads.fastq:
mason illumina -n 1000 -pmmf errors.txt -pmms 0.5 \
-sq -o myreads.fastq drosophila.genom
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