Provided by: art-nextgen-simulation-tools_20160605+dfsg-4build2_amd64 
NAME
art_illumina - Simulation of Illumina sequencers
DESCRIPTION
ART is a set of simulation tools to generate synthetic next-generation sequencing reads.
ART simulates sequencing reads by mimicking real sequencing process with empirical error
models or quality profiles summarized from large recalibrated sequencing data.
art_illumina can be used for Simulation of Illumina sequencers
USAGE
art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -ss
<sequencing_system> -o <outfile_prefix>
art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -o
<outfile_prefix>
art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -c <total_num_reads> -o
<outfile_prefix>
art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -m
<mean_fragsize> -s <std_fragsize> -o <outfile_prefix>
art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -c <total_num_reads> -m
<mean_fragsize> -s <std_fragsize> -o <outfile_prefix>
OPTIONS
-1 --qprof1
the first-read quality profile
-2 --qprof2
the second-read quality profile
-amp --amplicon amplicon sequencing simulation
-c --rcount
total number of reads/read pairs to be generated [per amplicon if for amplicon
simulation](not be used together with -f/--fcov)
-d --id
the prefix identification tag for read ID
-ef --errfree
indicate to generate the zero sequencing errors SAM file as well the regular one
NOTE: the reads in the zero-error SAM file have the same alignment positions as
those in the regular SAM file, but have no sequencing errors
-f --fcov
the fold of read coverage to be simulated or number of reads/read pairs generated
for each amplicon
-h --help
print out usage information
-i --in
the filename of input DNA/RNA reference
-ir --insRate
the first-read insertion rate (default: 0.00009)
-ir2 --insRate2 the second-read insertion rate (default: 0.00015)
-dr --delRate
the first-read deletion rate (default: 0.00011)
-dr2 --delRate2 the second-read deletion rate (default: 0.00023)
-l --len
the length of reads to be simulated
-m --mflen
the mean size of DNA/RNA fragments for paired-end simulations
-mp --matepair indicate a mate-pair read simulation
-nf --maskN
the cutoff frequency of 'N' in a window size of the read length for masking genomic
regions
NOTE: default: '-nf 1' to mask all regions with 'N'. Use '-nf 0' to turn off
masking
-na --noALN
do not output ALN alignment file
-o --out
the prefix of output filename
-p --paired
indicate a paired-end read simulation or to generate reads from both ends of
amplicons
NOTE: art will automatically switch to a mate-pair simulation if the given mean
fragment size >= 2000
-q --quiet
turn off end of run summary
-qs --qShift
the amount to shift every first-read quality score by
-qs2 --qShift2
the amount to shift every second-read quality score by
NOTE: For -qs/-qs2 option, a positive number will shift up quality scores (the max
is 93) that reduce substitution sequencing errors and a negative number will shift
down quality scores that increase sequencing errors. If shifting scores by x, the
error rate will be 1/(10^(x/10)) of the default profile.
-rs --rndSeed
the seed for random number generator (default: system time in second)
NOTE: using a fixed seed to generate two identical datasets from different runs
-s --sdev
the standard deviation of DNA/RNA fragment size for paired-end simulations.
-sam --samout
indicate to generate SAM alignment file
-sp --sepProf
indicate to use separate quality profiles for different bases (ATGC)
-ss --seqSys
The name of Illumina sequencing system of the built-in profile used for simulation
NOTE: sequencing system id names are:
GA1 - Genome Analyzer I, GA2 - Genome Analyzer II
HS10 - HiSeq 1000, HS20 - HiSeq 2000, HS25 - HiSeq 2500, MS - MiSeq
-M --cigarM
indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch
NOTES
* ART by default selects a built-in quality score profile according to the read length
specified for the run.
* For single-end simulation, ART requires input sequence file, outputfile prefix, read
length, and read count/fold coverage.
* For paired-end simulation (except for amplicon sequencing), ART also requires the
parameter values of
the mean and standard deviation of DNA/RNA fragment lengths
EXAMPLES
1) single-end read simulation
art_illumina -sam -i reference.fa -l 150 -ss HS25 -f 10 -o single_dat
2) paired-end read simulation
art_illumina -sam -i reference.fa -p -l 150 -ss HS25 -f 20 -m 200 -s 10 -o
paired_dat
3) mate-pair read simulation
art_illumina -sam -i reference.fa -mp -l 50 -f 20 -m 2500 -s 50 -o matepair_dat
4) amplicon sequencing simulation with 5' end single-end reads
art_illumina -amp -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_5end_dat
5) amplicon sequencing simulation with paired-end reads
art_illumina -amp -p -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_pair_dat
6) amplicon sequencing simulation with matepair reads
art_illumina -amp -mp -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_mate_dat
7) generate an extra SAM file with zero-sequencing errors for a paired-end read simulation
art_illumina -ef -i reference.fa -p -l 50 -f 20 -m 200 -s 10 -o paired_twosam_dat
8) reduce the substitution error rate to one 10th of the default profile
art_illumina -i reference.fa -qs 10 -qs2 10 -l 50 -f 10 -p -m 500 -s 10 -sam -o
reduce_error
9) turn off the masking of genomic regions with unknown nucleotides 'N'
art_illumina -nf 0 -sam -i reference.fa -p -l 50 -f 20 -m 200 -s 10 -o
paired_nomask
10) masking genomic regions with >=5 'N's within the read length 50
art_illumina -nf 5 -sam -i reference.fa -p -l 50 -f 20 -m 200 -s 10 -o
paired_maskN5
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for
any other usage of the program.