ARTFASTQGENERATOR(1)

✨ ARTFASTQGENERATOR ✨

okay bestie, gather round, because today we're talking about artfastqgenerator — the User Commands girlie that makes fake FASTQ files out of a reference genome 💖

🌸 NAME 🌸

artfastqgenerator — outputs artificial FASTQ files derived from a reference genome 🧬✨

🦋 SYNOPSIS 🦋

artfastqgenerator -O <outputPath> -R <referenceGenomePath> -S
<startSequenceIdentifier> -F1 <fastq1ForQualityScores> -F2
<fastq2ForQualityScores> -CMGCS <coverageMeanGCcontentSpread> -CMP
<coverageMeanPeak> -CMPGC <coverageMeanPeakGCcontent> -CSD <coverageSD>
-E <endSequenceIdentifier> -GCC <GCcontentBasedCoverage> -GCR
<GCcontentRegionSize> -L <logRegionStats> -N <nucleobaseBufferSize> -OF
<outputFormat> -RCNF <readsContainingNfilter> -RL <readLength> -SE
<simulateErrorInRead> -TLM <templateLengthMean> -TLSD <templateLengthSD>
-URQS <useRealQualityScores> -X <xStart> -Y <yStart>

like, that's a lot of flags, but she's worth it, no cap 💅

💜 DESCRIPTION 💜

ArtificialFastqGenerator takes your reference genome — in FASTA format — as input, and spits out artificial FASTQ files in the Sanger format. iconic behaviour honestly 🎀

She can also accept Phred base quality scores from existing FASTQ files, and use them to simulate sequencing errors. the way that works?? obsessed ✨

and here's the slay: since the artificial FASTQs are derived from the reference genome, the reference genome is basically the gold-standard for calling variants — we're talking Single Nucleotide Polymorphisms (SNPs) and insertions and deletions (indels) 🌈

which means you can evaluate a Next Generation Sequencing (NGS) analysis pipeline that aligns reads to the reference genome and then calls the variants. main character energy for real 👑

🎀 OPTIONS 🎀

• -h — Print usage help. (short, sweet, helpful, we love her 🫶)
• -O, <outputPath> — Path for the artificial fastq and log files, including their base name. must be specified ⚠️
• -R, <referenceGenomePath> — Reference genome sequence file. must be specified ⚠️
• -S, <startSequenceIdentifier> — Prefix of the sequence identifier in the reference after which read generation should begin. must be specified ⚠️
• -F1, <fastq1ForQualityScores> — First fastq file to use for real quality scores. must be specified if useRealQualityScores = true ⚠️
• -F2, <fastq2ForQualityScores> — Second fastq file to use for real quality scores. must be specified if useRealQualityScores = true ⚠️
• -CMGCS, <coverageMeanGCcontentSpread> — The spread of coverage mean given GC content. (default = 0.22) 📊
• -CMP, <coverageMeanPeak> — The peak coverage mean for a region. (default = 37.7) 📈
• -CMPGC, <coverageMeanPeakGCcontent> — The GC content for regions with peak coverage mean. (default = 0.45) 🧪
• -CSD, <coverageSD> — The coverage standard deviation divided by the mean. (default = 0.2) 📉
• -E, <endSequenceIdentifier> — Prefix of the sequence identifier in the reference where read generation should stop. (default = end of file) 🛑
• -GCC, <GCcontentBasedCoverage> — Whether nucleobase coverage is biased by GC content. (default = true) 🧬
• -GCR, <GCcontentRegionSize> — Region size in nucleobases for which to calculate GC content. (default = 150) 📏
• -L, <logRegionStats> — The region size as a multiple of -NBS for which summary coverage statistics are recorded. (default = 2) 📝
• -N, <nucleobaseBufferSize> — The number of reference sequence nucleobases to buffer in memory. (default = 5000) 🧠
• -OF, <outputFormat> — 'default': standard fastq output; 'debug_nucleobases(_nuc|read_ids)': debugging. 🐛
• -RCNF, <readsContainingNfilter> — Filter out no "N-containing" reads (0), "all-N" reads (1), "at-least-1-N" reads (2). (default = 0) 🚰
• -RL, <readLength> — The length of each read. (default = 76) 📐
• -SE, <simulateErrorInRead> — Whether to simulate error in the read based on the quality scores. (default = false) 😭
• -TLM, <templateLengthMean> — The mean DNA template length. (default = 210) 🧵
• -TLSD, <templateLengthSD> — The standard deviation of the DNA template length. (default = 60) 🎢
• -URQS, <useRealQualityScores> — Whether to use real quality scores from existing fastq files or set all to the maximum. (default = false) ⭐
• -X, <xStart> — The first read's X coordinate. (default = 1000) 🗺️
• -Y, <yStart> — The first read's Y coordinate. (default = 1000) 🧭

💀 BUGS 💀

Any bugs should be reported to Matthew.Frampton@icr.ac.uk — pls be nice, they're doing their best 🙈

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 💖

and that's the whole vibe check bestie — this is artfastqgenerator 0.0.20150519, dated February 2016, serving User Commands realness and living her best life in the ARTFASTQGENERATOR(1) section 💅✨ periodt 🎀