ART_454(1) User Commands ART_454(1)

art_454 - Simulation of 454 Pyrosequencing

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.

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

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>

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>

#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)

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.

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

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

February 2016 art_454 3.19.15