NAME

       art_SOLiD - Simulation of Applied Biosystems SOLiD Sequencing

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_SOLiD can be used for Simulation of Applied Biosystems SOLiD Sequencing.

USAGE

   SINGLE-END (F3 READ) SIMULATION
       art_SOLiD [ options ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <FOLD_COVERAGE>

   MATE-PAIR READS (F3-R3 PAIR) SIMULATION
       art_SOLiD  [  options  ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <FOLD_COVERAGE> <MEAN_FRAG_LEN>
       <STD_DEV>

   PAIRED-END READS (F3-F5 PAIR) SIMULATION
       art_SOLiD [ options ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ_F3>  <LEN_READ_F5>  <FOLD_COVERAGE>
       <MEAN_FRAG_LEN> <STD_DEV>

   AMPLICON SEQUENCING SIMULATION
       art_SOLiD [ options ] -A s <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <READS_PER_AMPLICON>

       art_SOLiD [ options ] -A m <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <LEN_READ> <READ_PAIRS_PER_AMPLICON>

       art_SOLiD   [   options   ]   -A  p  <INPUT_SEQ_FILE>  <OUTPUT_FILE_PREFIX>  <LEN_READ_F3>  <LEN_READ_F5>
       <READ_PAIRS_PER_AMPLICON>

OPTIONS

   MANDATORY OPTIONS
       INPUT_SEQ_FILE            -  filename of DNA/RNA reference sequences in FASTA format

       OUTPUT_FILE_PREFIX        -  prefix or directory for all output read data files

       FOLD_COVERAGE             -  fold of read coverage over the reference sequences

       LEN_READ                  -  length of F3/R3 reads

       LEN_READ_F3               -  length of F3 reads for paired-end read simulation

       LEN_READ_F5               -  length of F5 reads for paired-end read simulation

       READS_PER_AMPLICON        -  number of reads per amplicon

       READ_PAIRS_PER_AMPLICON   -  number of read pairs per amplicon

       MEAN_FRAG_LEN             -  mean DNA/RNA fragment size for matepair/paired-end read simulation

       STD_DEV                   -  standard deviation of the DNA/RNA  fragment  sizes  for  matepair/paired-end
       read simulation

   OPTIONAL PARAMETERS
       -A specify the read type for amplicon sequencing simulation (s:single-end, m: matepair, p: paired-end)

       -M indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch

       -s indicate to generate a SAM alignment file

       -r specify the random seed for the simulation

       -f specify the scale factor adjusting error rate (e.g., -f 0 for zero-error rate simulation)

       -p specify user's own read profile for simulation

EXAMPLES

       1) singl-end 25bp reads simulation at 10X coverage

              art_SOLiD -s seq_reference.fa ./outdir/single_dat 25 10

       2) singl-end 75bp reads simulation at 20X coverage with user's error profile

              art_SOLiD -s -p ../SOLiD_profiles/profile_pseudo ./seq_reference.fa ./dat_userProfile 75 20

       3)  matepair 35bp (F3-R3) reads simulation at 20X coverage with DNA/RNA MEAN fragment size 2000bp and STD
       50

              art_SOLiD -s seq_reference.fa ./outdir/matepair_dat 35 20 2000 50

       4) matepair reads simulation with a fixed random seed

              art_SOLiD -r 777 -s seq_reference.fa ./outdir/matepair_fs 50 10 1500 50

       5) paired-end reads (75bp F3, 35bp F5) simulation with the MEAN fragment size  250  and  STD  10  at  20X
       coverage

              art_SOLiD -s seq_reference.fa ./outdir/paired_dat 75 35 50 250 10

       6) amplicon sequencing with 25bp single-end reads at 100 reads per amplicon

              art_SOLiD -A s -s amp_reference.fa ./outdir/amp_single 25 100

       7) amplicon sequencing with 50bp matepair reads at 80 read pairs per amplicon

              art_SOLiD -A m -s amp_reference.fa ./outdir/amp_matepair 50 80

       8) amplicon sequencing with paired-end reads (35bp F3, 25bp F5 reads) at 50 pairs per amplicon

              art_SOLiD -A p -s amp_reference.fa ./outdir/amp_pair 35 25 50

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.