CATFISHQ(1)

👑 CATFISHQ 👑

okay so bestie, welcome to catfishq from the User Commands corner of the manual 💖 it's a lil command-line girlie that concatenates fastq files, and she eats long lists for breakfast. no cap.

✨ NAME ✨

catfishq — concatenates fastq files 🐟

🦋 DESCRIPTION 🦋

usage: here's exactly how you call her, character for character, no notes:

usage: catfishq [-h]
              [--log {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical}]
              [-o OUT] [-l MIN_LEN] [-q MIN_QSCORE] [--max-sequencing-time
              MAX_SEQ_TIME] [--min-sequencing-time MIN_SEQ_TIME] [--start-time
              START_TIME] [--print-start-time] [-n MAX_N] [-b MAX_BP] [-r] [-d]
              FASTQ [FASTQ ...]

Cat long lists of FASTQ files 💅 that's the whole vibe. she's literally built for the long list.

🌸 OPTIONS 🌸

🎀 positional arguments:

• FASTQ — the FASTQ files, or folders that are full of FASTQ files. hand her a whole pile, she's not scared 🫶

💜 optional arguments:

• -h, --help — show this help message and exit. the classic escape hatch, iconic.
• --log {DEBUG,INFO,WARNING,ERROR,CRITICAL,debug,info,warning,error,critical} — Print debug information. yes, both the shouty uppercase levels and the lowercase ones, all of them, exactly those.
• -o OUT, --output OUT — Output file. (default: stdout) — so if you don't say anything, she just yells into your terminal 😭
• -l MIN_LEN, --min-length MIN_LEN — Minimum read length.
• -q MIN_QSCORE, --min-qscore MIN_QSCORE — Minimum q-score.
• --max-sequencing-time MAX_SEQ_TIME — Only output reads that where sequenced up to the given time (minutes). ⏰
• --min-sequencing-time MIN_SEQ_TIME — Only output reads that where sequenced after the given time (minutes). ⏰
• --start-time START_TIME — Starttime of the run as guppy time stamp (only required with --sequencing-time). If 'min' is given as argument the minimal time is detected automatically. lowkey magic.
• --print-start-time — Print the minimal start_time of all fastq files.
• -n MAX_N, --max_n MAX_N — Stop after <max_n> reads.
• -b MAX_BP, --max_mbp MAX_BP — Stop after <max_bp> mega base pairs.
• -r, --recursive — Search folders recursively. go deeper bestie 🌈
• -d, --dedup — Remove duplicated reads. we do not do repeats in this house 💅

🧚 AUTHOR 🧚

This manpage was written by Steffen Moeller for the Debian distribution and can be used for any other usage of the program. king behavior, honestly 👑

and that's the whole page, bestie!! 💖 this was catfishq 1.1.3+ds, dated May 2021, and she's still serving. go concat something iconic ✨🦋🎀