QCAT(1)

💖 QCAT(1) — the manual, but make it slay 💖

okay bestie, pull up a chair, we're learning qcat and honestly? it's giving iconic. this is the User Commands page for qcat, version 1.1.0, and by the end of this you're gonna be demultiplexing like it's nothing. periodt.

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✨ NAME ✨

qcat — demultiplexing Oxford Nanopore reads from FASTQ files

ngl the name is short but the power is enormous 🦋

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🌸 SYNOPSIS 🌸

usage: qcat [-h] [-V] [-l LOG] [--quiet] [-f FASTQ] [-b BARCODE_DIR]
       [-o OUTPUT] [--min-score MIN_QUAL] [--detect-middle] [-t THREADS]
       [--min-read-length MIN_LENGTH] [--tsv] [--trim] [-k
       {Auto,RAB204,RPB004/RLB001,NBD104/NBD114,
        RAB204/RAB214,VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,
        RAB214,RBK004,PBC096,RBK001,NBD114,DUAL}] [--list-kits] [--guppy
       | --epi2me | --dual | --simple] [--no-batch] [--filter-barcodes]
       [--simple-barcodes SIMPLE_BARCODES]

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💅 DESCRIPTION 💅

so basically it's a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files. that's the whole vibe. reads go in, sorted reads come out, you feel like a genius. 🧚

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🎀 OPTIONS 🎀

options:

• -h, --help — shows this help message and then dips. classic.
• -V, --version — shows the program's version number and exits. little flex.
• -l LOG, --log LOG — prints debug information. when you need to see everything 👀
• --quiet — don't print the summary. shy mode. 🙈

General settings:

• -f FASTQ, --fastq FASTQ — barcoded read file. your input, your main character.
• -b BARCODE_DIR, --barcode_dir BARCODE_DIR — if you specify this, qcat will demultiplex reads into this folder. like, it'll make the folder situation happen for you 🫶
• -o OUTPUT, --output OUTPUT — the output file that trimmed reads get written to. default is stdout.
• --min-score MIN_QUAL — minimum barcode score. any barcode call scoring lower than this gets discarded, no hesitation, no apology. must be between 0 and 100. default is 60.
• --detect-middle — search for adapters in the whole read. not just the ends, the entire thing. thorough queen.
• -t THREADS, --threads THREADS — number of threads. heads up: only works in guppy mode.
• --min-read-length MIN_LENGTH — reads shorter than <min-read-length> after trimming get discarded. bye.
• --tsv — prints a tsv file containing barcode information for each read to stdout.
• --trim — removes adapter and barcode sequences from reads. decluttering ✨
• -k, --kit {Auto,RAB204,RPB004/RLB001,NBD104/NBD114,RAB204/RAB214,VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,RAB214,RBK004,PBC096,RBK001,NBD114,DUAL} — sequencing kit. specifying the correct kit will improve sensitivity and specificity and runtime. default is auto.
• --list-kits — lists all supported kits. window shopping 🛍️

Demultiplexing modes:

• --guppy — use Guppy's demultiplexing algorithm. default: false.
• --epi2me — use EPI2ME's demultiplexing algorithm. default: true. she's the default for a reason 💁
• --dual — use the dual barcoding algorithm.
• --simple — use the simple demultiplexing algorithm. it only looks for barcodes, not for adapter sequences.

⚠️ okay so --simple is for testing purposes only! do not make it your whole personality. 💀

EPI2ME options (only valid with --epi2me):

• --no-batch — don't use information from multiple reads for kit detection. default: false.
• --filter-barcodes — filter rare barcode calls when running in batch mode.

Simple options (only valid with --simple):

• --simple-barcodes SIMPLE_BARCODES — use 12 (standard) or 96 (extended) barcodes for demultiplexing.

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and that's the whole page bestie, no notes, 10/10, ate and left no crumbs 👑

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this lil manual? it's for qcat 1.1.0, dated November 2022, and it came to you straight from the User Commands section of the manual. mwah 💋 go demultiplex something gorgeous.