READUCKS(1)

💅 READUCKS(1) — Nanopore read de-multiplexer

okay so bestie, welcome to READUCKS(1) — that's the manual page for readucks, the read de-multiplexer ✨ (read demux -> readux -> readucks, innit). Yeah the name evolved like a group chat nickname. We love a glow-up. 🦋

🌸 SYNOPSIS

readucks -i INPUT_PATH [-o OUTPUT_DIR] [-b] [-a] [-e] [-s] [-m MODE]
        [-p PREFIX] [-t THREADS] [-n NUM_READS_IN_BATCH]
        [--check_reads CHECK_READS] [--adapter_threshold ADAPTER_THRESHOLD]
        [-v VERBOSITY] [--require_two_barcodes] [--report_alternate_call]
        [--native_barcodes] [--pcr_barcodes] [--rapid_barcodes]
        [--limit_barcodes_to LIMIT_BARCODES_TO [LIMIT_BARCODES_TO ...]]
        [--threshold THRESHOLD] [--secondary_threshold SECONDARY_THRESHOLD]
        [--score_diff SCORE_DIFF] [--scoring_scheme SCORING_SCHEME]
        [-h] [--version]

💖 DESCRIPTION

Readucks: a simple demuxing tool for nanopore data. That's it, that's the whole vibe check. ✨

🎀 Main options:

• -i INPUT_PATH, --input INPUT_PATH — FASTQ of input reads, or a directory that gets recursively searched for FASTQ files. This one is required bestie, no skipping it. 🚨
• -o OUTPUT_DIR, --output_dir OUTPUT_DIR — Where the output goes. (default: working directory)
• -b, --bin_barcodes — Reads get binned based on their barcode and saved to separate files. (default: False)
• -a, --annotate_files — Writes a CSV file for each input file containing barcode calls for each read. (default: False)
• -e, --extended_info — Writes extended information about barcode calls. (default: False)
• -s, --summary_info — Writes another file with information about barcode calls. (default: False)
• -m MODE, --mode MODE — Demuxing mode, one of ["stringent","lenient", "porechop"]. (default: porechop)
• -p PREFIX, --prefix PREFIX — Optional prefix to file names 🏷️
• -t THREADS, --threads THREADS — The number of threads to use (1 to turn off multithreading). (default: 2)
• -n NUM_READS_IN_BATCH, --num_reads_in_batch NUM_READS_IN_BATCH — The number of reads to process (and hold in memory) at a time. (default: 200)
• --check_reads CHECK_READS — Number of barcodes to classify before filtering barcode set. (default: 1000)
• --adapter_threshold ADAPTER_THRESHOLD — Identity required for a barcode to be included after filtering. (default: 90)
• -v VERBOSITY, --verbosity VERBOSITY — Level of output information: 0 = none, 1 = some, 2 = lots. (default: 1)

🌈 Demuxing options:

• --require_two_barcodes — Match barcodes at both ends of read (default single)
• --report_alternate_call — Reports double/single barcode call to csv in single/double barcoding mode (default: False)
• --native_barcodes — Only attempts to match the 24 native barcodes (default)
• --pcr_barcodes — Only attempts to match the 96 PCR barcodes (default: False)
• --rapid_barcodes — Only attempts to match the 12 rapid barcodes (default: False)
• --limit_barcodes_to LIMIT_BARCODES_TO [LIMIT_BARCODES_TO ...] — Specify a list of barcodes to look for (numbers refer to native, PCR or rapid)

🧚 Barcode search settings:

Settings for how to search for and call barcodes

• --threshold THRESHOLD — A read must have at least this percent identity to a barcode. (default: 75)
• --secondary_threshold SECONDARY_THRESHOLD — The second barcode must have at least this percent identity (and match the first one). (default: 65)
• --score_diff SCORE_DIFF — The second barcode must have at least this percent identity (and match the first one). (default: 5)

🙈 not me noticing that --score_diff has literally the exact same sentence as --secondary_threshold — that's what the docs say, so that's what I'm telling you. No cap. We report, we don't rewrite.

• --scoring_scheme SCORING_SCHEME — Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend. (default: 3,-6,-5,-2)

👑 Help:

• -h, --help — Show this help message and exit
• --version — Show program's version number and exit

⭐ AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. 🫶

and that's the whole page bestie, you ate that. this was readucks version 0.0.3, dated June 2020, living in the User Commands section of the manual. go forth and demultiplex, periodt. 💜