.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3. .TH ART_SOLID "1" "February 2016" "art_SOLiD 3.19.15" "User Commands" .SH NAME art_SOLiD \- Simulation of Applied Biosystems SOLiD Sequencing .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_SOLiD can be used for Simulation of Applied Biosystems SOLiD Sequencing. .SH USAGE .SS SINGLE\-END (F3 READ) SIMULATION .B art_SOLiD [ options ] .SS MATE\-PAIR READS (F3\-R3 PAIR) SIMULATION .B art_SOLiD [ options ] .SS PAIRED\-END READS (F3\-F5 PAIR) SIMULATION .B art_SOLiD [ options ] .SS AMPLICON SEQUENCING SIMULATION .B art_SOLiD [ options ] \fB\-A\fR s .P .B art_SOLiD [ options ] \fB\-A\fR m .P .B art_SOLiD [ options ] \fB\-A\fR p .SH OPTIONS .SS MANDATORY OPTIONS .TP INPUT_SEQ_FILE \- filename of DNA/RNA reference sequences in FASTA format .TP OUTPUT_FILE_PREFIX \- prefix or directory for all output read data files .TP FOLD_COVERAGE \- fold of read coverage over the reference sequences .TP LEN_READ \- length of F3/R3 reads .TP LEN_READ_F3 \- length of F3 reads for paired\-end read simulation .TP LEN_READ_F5 \- length of F5 reads for paired\-end read simulation .TP READS_PER_AMPLICON \- number of reads per amplicon .TP READ_PAIRS_PER_AMPLICON \- number of read pairs per amplicon .TP MEAN_FRAG_LEN \- mean DNA/RNA fragment size for matepair/paired\-end read simulation .TP STD_DEV \- standard deviation of the DNA/RNA fragment sizes for matepair/paired\-end read simulation .SS OPTIONAL PARAMETERS .TP \fB\-A\fR specify the read type for amplicon sequencing simulation (s:single\-end, m: matepair, p: paired\-end) .TP \fB\-M\fR indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch .TP \fB\-s\fR indicate to generate a SAM alignment file .TP \fB\-r\fR specify the random seed for the simulation .TP \fB\-f\fR specify the scale factor adjusting error rate (e.g., \fB\-f\fR 0 for zero\-error rate simulation) .TP \fB\-p\fR specify user's own read profile for simulation .SH EXAMPLES .TP 1) singl\-end 25bp reads simulation at 10X coverage .IP art_SOLiD \fB\-s\fR seq_reference.fa ./outdir/single_dat 25 10 .TP 2) singl\-end 75bp reads simulation at 20X coverage with user's error profile .IP art_SOLiD \fB\-s\fR \fB\-p\fR ../SOLiD_profiles/profile_pseudo ./seq_reference.fa ./dat_userProfile 75 20 .TP 3) matepair 35bp (F3\-R3) reads simulation at 20X coverage with DNA/RNA MEAN fragment size 2000bp and STD 50 .IP art_SOLiD \fB\-s\fR seq_reference.fa ./outdir/matepair_dat 35 20 2000 50 .TP 4) matepair reads simulation with a fixed random seed .IP art_SOLiD \fB\-r\fR 777 \fB\-s\fR seq_reference.fa ./outdir/matepair_fs 50 10 1500 50 .TP 5) paired\-end reads (75bp F3, 35bp F5) simulation with the MEAN fragment size 250 and STD 10 at 20X coverage .IP art_SOLiD \fB\-s\fR seq_reference.fa ./outdir/paired_dat 75 35 50 250 10 .TP 6) amplicon sequencing with 25bp single\-end reads at 100 reads per amplicon .IP art_SOLiD \fB\-A\fR s \fB\-s\fR amp_reference.fa ./outdir/amp_single 25 100 .TP 7) amplicon sequencing with 50bp matepair reads at 80 read pairs per amplicon .IP art_SOLiD \fB\-A\fR m \fB\-s\fR amp_reference.fa ./outdir/amp_matepair 50 80 .TP 8) amplicon sequencing with paired\-end reads (35bp F3, 25bp F5 reads) at 50 pairs per amplicon .IP art_SOLiD \fB\-A\fR p \fB\-s\fR amp_reference.fa ./outdir/amp_pair 35 25 50 .SH AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.