art_SOLiD1

Simulation of applied biosystems solid sequencing

Overview

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13