.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH ART_ILLUMINA "1" "February 2016" "art_illumina 3.19.15" "User Commands"
.SH NAME
art_illumina \- Simulation of Illumina sequencers
.SH 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.
.P
art_illumina can be used for Simulation of Illumina sequencers
.SH USAGE
.B art_illumina
[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-f\fR <fold_coverage> \fB\-ss\fR <sequencing_system> \fB\-o\fR <outfile_prefix>
.P
.B art_illumina
[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-f\fR <fold_coverage> \fB\-o\fR <outfile_prefix>
.P
.B art_illumina
[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-c\fR <total_num_reads> \fB\-o\fR <outfile_prefix>
.P
.B art_illumina
[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-f\fR <fold_coverage> \fB\-m\fR <mean_fragsize> \fB\-s\fR <std_fragsize> \fB\-o\fR <outfile_prefix>
.P
.B art_illumina
[options] \fB\-sam\fR \fB\-i\fR <seq_ref_file> \fB\-l\fR <read_length> \fB\-c\fR <total_num_reads> \fB\-m\fR <mean_fragsize> \fB\-s\fR <std_fragsize> \fB\-o\fR <outfile_prefix>
.SH OPTIONS
.TP
\fB\-1\fR   \fB\-\-qprof1\fR
the first\-read quality profile
.TP
\fB\-2\fR   \fB\-\-qprof2\fR
the second\-read quality profile
.HP
\fB\-amp\fR \fB\-\-amplicon\fR amplicon sequencing simulation
.TP
\fB\-c\fR   \fB\-\-rcount\fR
total number of reads/read pairs to be generated [per amplicon if for amplicon simulation](not be used together with \fB\-f\fR/\-\-fcov)
.TP
\fB\-d\fR   \fB\-\-id\fR
the prefix identification tag for read ID
.TP
\fB\-ef\fR  \fB\-\-errfree\fR
indicate to generate the zero sequencing errors SAM file as well the regular one
.IP
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
.TP
\fB\-f\fR   \fB\-\-fcov\fR
the fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon
.TP
\fB\-h\fR   \fB\-\-help\fR
print out usage information
.TP
\fB\-i\fR   \fB\-\-in\fR
the filename of input DNA/RNA reference
.TP
\fB\-ir\fR  \fB\-\-insRate\fR
the first\-read insertion rate (default: 0.00009)
.HP
\fB\-ir2\fR \fB\-\-insRate2\fR the second\-read insertion rate (default: 0.00015)
.TP
\fB\-dr\fR  \fB\-\-delRate\fR
the first\-read deletion rate (default:  0.00011)
.HP
\fB\-dr2\fR \fB\-\-delRate2\fR the second\-read deletion rate (default: 0.00023)
.TP
\fB\-l\fR   \fB\-\-len\fR
the length of reads to be simulated
.TP
\fB\-m\fR   \fB\-\-mflen\fR
the mean size of DNA/RNA fragments for paired\-end simulations
.HP
\fB\-mp\fR  \fB\-\-matepair\fR indicate a mate\-pair read simulation
.TP
\fB\-nf\fR  \fB\-\-maskN\fR
the cutoff frequency of 'N' in a window size of the read length for masking genomic regions
.IP
NOTE: default: '\-nf 1' to mask all regions with 'N'. Use '\-nf 0' to turn off masking
.TP
\fB\-na\fR  \fB\-\-noALN\fR
do not output ALN alignment file
.TP
\fB\-o\fR   \fB\-\-out\fR
the prefix of output filename
.TP
\fB\-p\fR   \fB\-\-paired\fR
indicate a paired\-end read simulation or to generate reads from both ends of amplicons
.IP
NOTE: art will automatically switch to a mate\-pair simulation if the given mean fragment size >= 2000
.TP
\fB\-q\fR   \fB\-\-quiet\fR
turn off end of run summary
.TP
\fB\-qs\fR  \fB\-\-qShift\fR
the amount to shift every first\-read quality score by
.TP
\fB\-qs2\fR \fB\-\-qShift2\fR
the amount to shift every second\-read quality score by
.IP
NOTE: For \fB\-qs\fR/\-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.
.TP
\fB\-rs\fR  \fB\-\-rndSeed\fR
the seed for random number generator (default: system time in second)
.IP
NOTE: using a fixed seed to generate two identical datasets from different runs
.TP
\fB\-s\fR   \fB\-\-sdev\fR
the standard deviation of DNA/RNA fragment size for paired\-end simulations.
.TP
\fB\-sam\fR \fB\-\-samout\fR
indicate to generate SAM alignment file
.TP
\fB\-sp\fR  \fB\-\-sepProf\fR
indicate to use separate quality profiles for different bases (ATGC)
.TP
\fB\-ss\fR  \fB\-\-seqSys\fR
The name of Illumina sequencing system of the built\-in profile used for simulation
.IP
NOTE: sequencing system id names are:
.TP
GA1 \- Genome Analyzer I, GA2 \- Genome Analyzer II
.TP
HS10 \- HiSeq 1000, HS20 \- HiSeq 2000, HS25 \- HiSeq 2500, MS \- MiSeq
.TP
\fB\-M\fR  \fB\-\-cigarM\fR
indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch
.SH NOTES
.PP
* ART by default selects a built\-in quality score profile according to the read length specified for the run.
.PP
* For single\-end simulation, ART requires input sequence file, outputfile prefix, read length, and read count/fold coverage.
.PP
* For paired\-end simulation (except for amplicon sequencing), ART also requires the parameter values of
.IP
the mean and standard deviation of DNA/RNA fragment lengths
.PP
.SH EXAMPLES
.TP
1) single\-end read simulation
.IP
art_illumina \fB\-sam\fR \fB\-i\fR reference.fa \fB\-l\fR 150 \fB\-ss\fR HS25 \fB\-f\fR 10 \fB\-o\fR single_dat
.TP
2) paired\-end read simulation
.IP
art_illumina \fB\-sam\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 150 \fB\-ss\fR HS25 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_dat
.TP
3) mate\-pair read simulation
.IP
art_illumina \fB\-sam\fR \fB\-i\fR reference.fa \fB\-mp\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 2500 \fB\-s\fR 50 \fB\-o\fR matepair_dat
.TP
4) amplicon sequencing simulation with 5' end single\-end reads
.IP
art_illumina \fB\-amp\fR \fB\-sam\fR \fB\-na\fR \fB\-i\fR amp_reference.fa \fB\-l\fR 50 \fB\-f\fR 10 \fB\-o\fR amplicon_5end_dat
.TP
5) amplicon sequencing simulation with paired\-end reads
.IP
art_illumina \fB\-amp\fR \fB\-p\fR \fB\-sam\fR \fB\-na\fR \fB\-i\fR amp_reference.fa \fB\-l\fR 50 \fB\-f\fR 10 \fB\-o\fR amplicon_pair_dat
.TP
6) amplicon sequencing simulation with matepair reads
.IP
art_illumina \fB\-amp\fR \fB\-mp\fR \fB\-sam\fR \fB\-na\fR \fB\-i\fR amp_reference.fa \fB\-l\fR 50 \fB\-f\fR 10 \fB\-o\fR amplicon_mate_dat
.TP
7) generate an extra SAM file with zero\-sequencing errors for a paired\-end read simulation
.IP
art_illumina \fB\-ef\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_twosam_dat
.TP
8) reduce the substitution error rate to one 10th of the default profile
.IP
art_illumina \fB\-i\fR reference.fa \fB\-qs\fR 10 \fB\-qs2\fR 10 \fB\-l\fR 50 \fB\-f\fR 10 \fB\-p\fR \fB\-m\fR 500 \fB\-s\fR 10 \fB\-sam\fR \fB\-o\fR reduce_error
.TP
9) turn off the masking of genomic regions with unknown nucleotides 'N'
.IP
art_illumina \fB\-nf\fR 0 \fB\-sam\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_nomask
.TP
10) masking genomic regions with >=5 'N's within the read length 50
.IP
art_illumina \fB\-nf\fR 5 \fB\-sam\fR \fB\-i\fR reference.fa \fB\-p\fR \fB\-l\fR 50 \fB\-f\fR 20 \fB\-m\fR 200 \fB\-s\fR 10 \fB\-o\fR paired_maskN5
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.