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.