ART_ILLUMINA(1)

✨ NAME ✨

art_illumina — simulation of Illumina sequencers 🧬💖

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🌸 DESCRIPTION 🌸

okay so bestie, ART is a whole suite of simulation tools that cook up synthetic next-generation sequencing reads for you. It doesn't just make stuff up out of nowhere either — it mimics the real sequencing process using empirical error models and quality profiles that were summarized from big piles of recalibrated sequencing data. no cap. 🔥

art_illumina specifically is your girl for Simulation of Illumina sequencers 👑

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🎀 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>

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💅 OPTIONS 💅

like, this is the good part. every single flag, all of them, periodt ✨

• -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) — so like, pick one, not both, bestie 💀
• -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. math is mathing 🧮

• -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 🎯

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🌈 NOTES 🌈

• ART by default selects a built-in quality score profile according to the read length specified for the run. it just knows ✨
• For single-end simulation, ART requires input sequence file, outputfile prefix, read length, and read count/fold coverage. that's the bare minimum bestie 🫶
• 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 🧬

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🔥 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

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👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, absolute legend 🫶💖

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and that's the whole thing bestie, we ate and left no crumbs 💅✨ this was art_illumina version 3.19.15, dated February 2016 — iconic behavior honestly, mwah 🎀🦋🌸