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

OPTIONS

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.