art_illumina1

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_illumina can be used for Simulation of Illumina sequencers

Usage

art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -ss <sequencing_system> -o <outfile_prefix>

art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -o <outfile_prefix>

art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -c <total_num_reads> -o <outfile_prefix>

art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -m <mean_fragsize> -s <std_fragsize> -o <outfile_prefix>

art_illumina [options] -sam -i <seq_ref_file> -l <read_length> -c <total_num_reads> -m <mean_fragsize> -s <std_fragsize> -o <outfile_prefix>

Options

-1 --qprof1

the first-read quality profile

-2 --qprof2

the second-read quality profile

-amp --amplicon amplicon sequencing simulation

-c --rcount

total number of reads/read pairs to be generated [per amplicon if for amplicon simulation](not be used together with -f/--fcov)

-d --id

the prefix identification tag for read ID

-ef --errfree

indicate to generate the zero sequencing errors SAM file as well the regular one

NOTE: the reads in the zero-error SAM file have the same alignment positions as those in the regular SAM file, but have no sequencing errors

-f --fcov

the fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon

-h --help

print out usage information

-i --in

the filename of input DNA/RNA reference

-ir --insRate

the first-read insertion rate (default: 0.00009)

-ir2 --insRate2 the second-read insertion rate (default: 0.00015)

-dr --delRate

the first-read deletion rate (default: 0.00011)

-dr2 --delRate2 the second-read deletion rate (default: 0.00023)

-l --len

the length of reads to be simulated

-m --mflen

the mean size of DNA/RNA fragments for paired-end simulations

-mp --matepair indicate a mate-pair read simulation

-nf --maskN

the cutoff frequency of 'N' in a window size of the read length for masking genomic regions

NOTE: default: '-nf 1' to mask all regions with 'N'. Use '-nf 0' to turn off masking

-na --noALN

do not output ALN alignment file

-o --out

the prefix of output filename

-p --paired

indicate a paired-end read simulation or to generate reads from both ends of amplicons

NOTE: art will automatically switch to a mate-pair simulation if the given mean fragment size >= 2000

-q --quiet

turn off end of run summary

-qs --qShift

the amount to shift every first-read quality score by

-qs2 --qShift2

the amount to shift every second-read quality score by

NOTE: For -qs/-qs2 option, a positive number will shift up quality scores (the max is 93) that reduce substitution sequencing errors and a negative number will shift down quality scores that increase sequencing errors. If shifting scores by x, the error rate will be 1/(10^(x/10)) of the default profile.

-rs --rndSeed

the seed for random number generator (default: system time in second)

NOTE: using a fixed seed to generate two identical datasets from different runs

-s --sdev

the standard deviation of DNA/RNA fragment size for paired-end simulations.

-sam --samout

indicate to generate SAM alignment file

-sp --sepProf

indicate to use separate quality profiles for different bases (ATGC)

-ss --seqSys

The name of Illumina sequencing system of the built-in profile used for simulation

NOTE: sequencing system id names are:

GA1 - Genome Analyzer I, GA2 - Genome Analyzer II

HS10 - HiSeq 1000, HS20 - HiSeq 2000, HS25 - HiSeq 2500, MS - MiSeq

-M --cigarM

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

Notes

* ART by default selects a built-in quality score profile according to the read length specified for the run.

* For single-end simulation, ART requires input sequence file, outputfile prefix, read length, and read count/fold coverage.

* For paired-end simulation (except for amplicon sequencing), ART also requires the parameter values of

the mean and standard deviation of DNA/RNA fragment lengths

Examples

1) single-end read simulation

art_illumina -sam -i reference.fa -l 150 -ss HS25 -f 10 -o single_dat

2) paired-end read simulation

art_illumina -sam -i reference.fa -p -l 150 -ss HS25 -f 20 -m 200 -s 10 -o paired_dat

3) mate-pair read simulation

art_illumina -sam -i reference.fa -mp -l 50 -f 20 -m 2500 -s 50 -o matepair_dat

4) amplicon sequencing simulation with 5' end single-end reads

art_illumina -amp -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_5end_dat

5) amplicon sequencing simulation with paired-end reads

art_illumina -amp -p -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_pair_dat

6) amplicon sequencing simulation with matepair reads

art_illumina -amp -mp -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_mate_dat

7) generate an extra SAM file with zero-sequencing errors for a paired-end read simulation

art_illumina -ef -i reference.fa -p -l 50 -f 20 -m 200 -s 10 -o paired_twosam_dat

8) reduce the substitution error rate to one 10th of the default profile

art_illumina -i reference.fa -qs 10 -qs2 10 -l 50 -f 10 -p -m 500 -s 10 -sam -o reduce_error

9) turn off the masking of genomic regions with unknown nucleotides 'N'

art_illumina -nf 0 -sam -i reference.fa -p -l 50 -f 20 -m 200 -s 10 -o paired_nomask

10) masking genomic regions with >=5 'N's within the read length 50

art_illumina -nf 5 -sam -i reference.fa -p -l 50 -f 20 -m 200 -s 10 -o paired_maskN5