ART_SOLID(1)

💅 art_SOLiD — the manual, but make it make sense

okay bestie, you found the art_SOLiD(1) page, it lives in the User Commands section, and honestly? it's a whole vibe. let's get into it 💖

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✨ NAME ✨

art_SOLiD — Simulation of Applied Biosystems SOLiD Sequencing 🧬✨

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🌸 DESCRIPTION 🌸

So. ART is a lil family of simulation tools, and what they do is generate synthetic next-generation sequencing reads. Like, fake reads that act real. 🎀

The way it pulls that off is by mimicking the actual real-life sequencing process — using empirical error models or quality profiles that were summarized from big ol' piles of recalibrated sequencing data. no cap, it's giving science. 🔥

And art_SOLiD specifically? She's the one you call when you want Simulation of Applied Biosystems SOLiD Sequencing. that's her whole job. periodt. 👑

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🦋 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>

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⭐ OPTIONS ⭐

Mandatory options (yes these are required, don't skip them bestie 😭)

• INPUT_SEQ_FILE — the filename of your DNA/RNA reference sequences, in FASTA format. it's the blueprint, the source material, the main character. 🧬
• OUTPUT_FILE_PREFIX — the prefix, or the directory, for all the output read data files. everything lands here. 📁
• FOLD_COVERAGE — the fold of read coverage over the reference sequences. how much you're covering it. the coverage. 💅
• LEN_READ — the length of the F3/R3 reads. how long they are. that's it, that's the info. 📏
• LEN_READ_F3 — the length of the F3 reads for paired-end read simulation. 🎀
• LEN_READ_F5 — the length of the F5 reads for paired-end read simulation. 🎀
• READS_PER_AMPLICON — the number of reads per amplicon. 🔢
• READ_PAIRS_PER_AMPLICON — the number of read pairs per amplicon. 🔢
• MEAN_FRAG_LEN — the mean DNA/RNA fragment size, for matepair/paired-end read simulation. the average, the moment, the mean. 📐
• STD_DEV — the standard deviation of the DNA/RNA fragment sizes, for matepair/paired-end read simulation. the spread, the chaos, the range. 🌈

Optional parameters (the fun little extras ✨)

• -A — specify the read type for amplicon sequencing simulation. your choices are s for single-end, m for matepair, and p for paired-end. pick your fighter 💫
• -M — indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch. ⚙️
• -s — indicate to generate a SAM alignment file. yes bestie, the SAM file. 🧾
• -r — specify the random seed for the simulation. reproducible girlies rise up 🌱
• -f — specify the scale factor adjusting error rate — for example, -f 0 gives you a zero-error rate simulation. flawless, error-free, iconic. ✨
• -p — specify your own read profile for the simulation. bring your own vibe. 🎧

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💀 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

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🫶 AUTHOR 🫶

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. shoutout to Andreas, absolute legend. 🙌

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and that's the whole page bestie, you ate that 🍓

okay so this is art_SOLiD version 3.19.15, dated February 2016 — go forth and simulate, mwah 💅💖✨