--- name: "art_illumina" 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_illumina" --- # art\_illumina(1) Simulation of Illumina sequencers ## NAME art\_illumina - Simulation of Illumina sequencers ## 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\_illumina can be used for Simulation of Illumina sequencers ## USAGE **art\_illumina** \[options\] **-sam** **-i** \ **-l** \ **-f** \ **-ss** \ **-o** \ **art\_illumina** \[options\] **-sam** **-i** \ **-l** \ **-f** \ **-o** \ **art\_illumina** \[options\] **-sam** **-i** \ **-l** \ **-c** \ **-o** \ **art\_illumina** \[options\] **-sam** **-i** \ **-l** \ **-f** \ **-m** \ **-s** \ **-o** \ **art\_illumina** \[options\] **-sam** **-i** \ **-l** \ **-c** \ **-m** \ **-s** \ **-o** \ ## 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 ## AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.