---
name: "art_SOLiD"
section: "1"
platform: "linux"
package: "art-nextgen-simulation-tools"
version: "20160605+dfsg-5+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/art_SOLiD"
---

# art\_SOLiD(1)

Simulation of Applied Biosystems SOLiD Sequencing

## 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.