NAME

       art_454 - Simulation of 454 Pyrosequencing

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_454 can be used for Simulation of 454 Pyrosequencing.

USAGE

   SINGLE-END SIMULATION
       art_454  [-s]  [-a  ]  [-t]  [-r  rand_seed]  [  -p  read_profile ] [ -c num_flow_cycles ]
       <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE>

   PAIRED-END SIMULATION
       art_454
        [-s]  [-a  ]  [-t]  [-r  rand_seed]  [  -p  read_profile  ]  [   -c   num_flow_cycles   ]
       <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE> <MEAN_FRAG_LEN> <STD_DEV>

   AMPLICON SEQUENCING SIMULATION
       art_454  [-s] [-a ] [-t] [-r rand_seed] [ -p read_profile ] [ -c num_flow_cycles ] <-A|-B>
       <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <#_READS/#_READ_PAIRS_PER_AMPLICON>

OPTIONS

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

       OUTPUT_FILE_PREFIX       -  the prefix or directory of output read data  file  (*.fq)  and
       read alignment file (*.aln)

       FOLD_COVERAGE            -  the fold of read coverage over the reference sequences

       MEAN_FRAG_LEN            -  the average DNA fragment size for paired-end read simulation

       STD_DEV                  -  the standard deviation of the DNA fragment size for paired-end
       read simulation

       #READS_PER_AMPLICON      -  number of reads per amplicon (for 5'end amplicon sequencing)

       #READ_PAIRS_PER_AMPLICON -  number of  read  pairs  per  amplicon  (for  two-end  amplicon
       sequencing)

   OPTIONAL PARAMETERS
       -A indicate to perform single-end amplicon sequencing simulation

       -B indicate to perform paired-end amplicon sequencing simulation

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

       -a indicate to output the ALN alignment file

       -s indicate to output the SAM alignment file

       -d print out warning messages for debugging

       -t  indicate  to simulate reads from the built-in GS FLX Titanium profile [default: GS FLX
       profile]

       -r specify a fixed random seed for the simulation (to generate two identical datasets from
       two different runs)

       -c  specify  the number of flow cycles by the sequencer [ default: 100 for GS-FLX, and 200
       for GS-FLX Titanium ]

       -p specify user's own read profile for simulation

       NOTE: the name of a read profile is the directory  containing  read  profile  data  files.
       please  read  the REAME file about the format of 454 read profile data files and.  and the
       default filenames of these data files.

EXAMPLES

       1) singl-end simulation with 20X coverage

              art_454 -s seq_reference.fa ./outdir/single_dat 20

       2) paired-end simulation with the mean fragment size 1500 and STD 20 using GS FLX Titanium
       platform

              art_454 -s -t seq_reference.fa ./outdir/paired_dat 10 1500 20

       3) paired-end simulation with a fixed random seed

              art_454 -s -r 777 seq_reference.fa ./outdir/paired_fxSeed 10 2500 50

       4) single-end amplicon sequencing with 10 reads per amplicon

              art_454 -A -s amplicon_ref.fa ./outdir/amp_single 10

       5) paired-end amplicon sequencing with 10 read pairs per amplicon

              art_454 -B -s amplicon_ref.fa ./outdir/amp_paired 10

AUTHOR

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