FASTQC(1)

💖 FASTQC 💖

ok so this is the fastqc page from section 1 of the User Commands manual, and bestie, we're about to make high-throughput sequence QC actually make sense. no cap. 🦋

✨ NAME ✨

FastQC — the high throughput sequence QC analysis tool. it's giving quality control, it's giving pipeline-ready, it's giving your sequencing data a full vibe check. 👑

🌸 SYNOPSIS 🌸

fastqc seqfile1 seqfile2 .. seqfileN

fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]

[-c contaminant file] seqfile1 .. seqfileN

💅 DESCRIPTION 💅

okay so here's the tea 🍓 — FastQC reads a whole set of sequence files and, for each one, produces a quality control report. That report is made up of a bunch of different modules, and every single module is out here trying to catch a different potential type of problem lurking in your data. it's a whole squad of tiny detectives. 🔍

and here's the part where it gets flexible: if you don't give it any files to process on the command line, the program just starts up as an interactive graphical application. but if you do hand it files on the command line, it runs with zero user interaction required — no clicking, no vibes, just results. in that mode it's literally built to slot right into a standardised analysis pipeline. main character energy fr fr. ✨

the options for the program are as follows (and yes, we're going through every single one, because we don't skip 💜):

🎀 OPTIONS 🎀

• -h, --help — prints this help file and dips. that's it, that's the whole job. 👋
• -v, --version — prints the version of the program and exits. know your era. 🏷️
• -o, --outdir — creates all the output files in the output directory you specify. ⚠️ but listen, bestie: that directory has to already exist — the program will not create it for you, so don't come crying. if you don't set this option, then the output file for each sequence file gets created in the same directory as the sequence file that got processed. same folder, no travel. 📁
• --casava — for when your files come from raw casava output. files in the same sample group (meaning they only differ by the group number) get analysed as a set instead of one by one. any sequences with the filter flag set in the header get excluded from the analysis entirely, bye 👋. and heads up: files must have the exact same names casava gave them — including being gzipped and ending in .gz — otherwise they won't group together correctly. naming matters, periodt. 💅
• --extract — if you set this, the zipped output file gets uncompressed in the same directory after it's been created. by default this option is set automatically if fastqc is run in non-interactive mode. 🫶
• -j, --java — gives the full path to the java binary you want to use to launch fastqc. if you don't supply it, then java is assumed to be sitting in your PATH. ☕
• --noextract — do not uncompress the output file after creating it. you want this one if you don't want the output uncompressed when you're running in non-interactive mode. keep it zipped, keep it cute. 🤐
• --nogroup — disables the grouping of bases for reads longer than 50bp. every report will then show data for every single base in the read. no skipping, no grouping, just all of it. 😤

WARNING: using this option will cause fastqc to crash and burn if you use it on really long reads, and your plots may end up a ridiculous size. you have been warned!! 💀🔥

• -f, --format — bypasses the normal sequence file format detection and forces the program to use the format you specify. the valid formats are bam, sam, bam_mapped, sam_mapped and fastq. pick your fighter. ⚔️
• -t, --threads — specifies the number of files that can be processed simultaneously. each thread gets allocated 250MB of memory, so don't run more threads than your available memory can cope with, and not more than 6 threads on a 32 bit machine. respect the RAM, it's sensitive. 🧠
• -c, --contaminants — specifies a non-default file containing the list of contaminants to screen overrepresented sequences against. the file must contain sets of named contaminants in the form name[tab]sequence. any lines prefixed with a hash get ignored. 🚫
• -k, --kmers — specifies the length of Kmer to look for in the Kmer content module. the specified Kmer length must be between 2 and 10. default length is 5 if you don't specify anything. ✨
• -q, --quiet — suppresses all progress messages on stdout and only reports errors. silence is golden, but errors still get through. 🤫

🐛 BUGS 🐛

any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk or in www.bioinformatics.babraham.ac.uk/bugzilla/. found a lil gremlin? tell the people. 📣

👑 AUTHOR 👑

this manpage was created using help2man by Andreas Tille <tille@debian.org> for the Debian distribution — but bestie, it can be used by others as well. sharing is caring. 🫶

and that's the whole page, babe! this was FastQC v0.10.1, dated November 2012 🌈 — oldie but an absolute icon, and it still eats. mwah. 💋✨🎀🦋🌸