ART_454(1)

👑 ART_454 — the 454 pyrosequencing simulator, bestie 👑

okay so before we do literally anything else: this page is ART_454(1), meaning it's a user command — the kind you actually type into your terminal, not some dusty section-3 library thing. and it's the manual for art_454, the 454 pyrosequencing simulator. let's go 🦋

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🌸 NAME 🌸

art_454 — Simulation of 454 Pyrosequencing

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✨ DESCRIPTION ✨

so, ART is a whole set of simulation tools whose job is to generate synthetic next-generation sequencing reads. it doesn't just make stuff up out of nowhere either — it simulates sequencing reads by mimicking the real sequencing process, using empirical error models or quality profiles that were summarized from large recalibrated sequencing data. it's giving ✨science✨ fr fr.

and art_454 specifically? that's the one you use for Simulation of 454 Pyrosequencing. that's its whole thing. that's the moment. 💅

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🎀 USAGE 🎀

💖 SINGLE-END SIMULATION 💖

art_454 [-s] [-a ] [-t] [-r rand_seed] [ -p read_profile ] [ -c num_flow_cycles ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE>

🦋 PAIRED-END SIMULATION 🦋

art_454 [-s] [-a ] [-t] [-r rand_seed] [ -p read_profile ] [ -c num_flow_cycles ] <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <FOLD_COVERAGE> <MEAN_FRAG_LEN> <STD_DEV>

🌈 AMPLICON SEQUENCING SIMULATION 🌈

art_454 [-s] [-a ] [-t] [-r rand_seed] [ -p read_profile ] [ -c num_flow_cycles ] <-A|-B> <INPUT_SEQ_FILE> <OUTPUT_FILE_PREFIX> <#_READS/#_READ_PAIRS_PER_AMPLICON>

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💅 OPTIONS 💅

⭐ MANDATORY OPTIONS ⭐

these ones? not optional. you will be providing them. periodt.

• INPUT_SEQ_FILE — the filename of your DNA/RNA reference sequences, in FASTA format. no file, no reads, no nothing. 🧚
• OUTPUT_FILE_PREFIX — the prefix (or the directory) for the output read data file (*.fq) and the read alignment file (*.aln). that's where your results go live. 🏠
• FOLD_COVERAGE — the fold of read coverage over the reference sequences. the depth, the drama, the coverage. 🔥
• MEAN_FRAG_LEN — the average DNA fragment size, used for paired-end read simulation.
• STD_DEV — the standard deviation of the DNA fragment size, also for paired-end read simulation. her and MEAN_FRAG_LEN are a package deal, iykyk. 🫶
• #READS_PER_AMPLICON — number of reads per amplicon (this one's for 5'end amplicon sequencing).
• #READ_PAIRS_PER_AMPLICON — number of read pairs per amplicon (this one's for two-end amplicon sequencing).

💜 OPTIONAL PARAMETERS 💜

the fun lil extras. sprinkle as needed:

• -A — indicate to perform single-end amplicon sequencing simulation
• -B — indicate to perform paired-end amplicon sequencing simulation
• -M — indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch
• -a — indicate to output the ALN alignment file
• -s — indicate to output the SAM alignment file
• -d — print out warning messages for debugging
• -t — indicate to simulate reads from the built-in GS FLX Titanium profile [default: GS FLX profile]
• -r — specify a fixed random seed for the simulation (this is the one you want if you're trying to generate two identical datasets from two different runs 👀)
• -c — specify the number of flow cycles by the sequencer [ default: 100 for GS-FLX, and 200 for GS-FLX Titanium ]
• -p — specify user's own read profile for simulation

NOTE: the name of a read profile is the directory containing read profile data files. please read the REAME file about the format of 454 read profile data files and. and the default filenames of these data files.

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🍓 EXAMPLES 🍓

1. singl-end simulation with 20X coverage

art_454 -s seq_reference.fa ./outdir/single_dat 20

2. paired-end simulation with the mean fragment size 1500 and STD 20 using GS FLX Titanium platform

art_454 -s -t seq_reference.fa ./outdir/paired_dat 10 1500 20

3. paired-end simulation with a fixed random seed

art_454 -s -r 777 seq_reference.fa ./outdir/paired_fxSeed 10 2500 50

4. single-end amplicon sequencing with 10 reads per amplicon

art_454 -A -s amplicon_ref.fa ./outdir/amp_single 10

5. paired-end amplicon sequencing with 10 read pairs per amplicon

art_454 -B -s amplicon_ref.fa ./outdir/amp_paired 10

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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.

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and that's the whole page, bestie!! 💖✨ this one is art_454 version 3.19.15, dated February 2016 — iconic behavior from a 2016 manpage honestly. go simulate some reads, you got this 👑🌸