UNICYCLER_CHECK(1)

📦 version 0.5.1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 UNICYCLER_CHECK(1) 💖

okay bestie, pull up a chair, we're reading the unicycler_check manual page together and honestly? it's giving ✨quality control✨. This is a User Command from the unicycler fam, and yes it's the long read assembly checker, and yes we're gonna get into it. 🦋

🌸 NAME 🌸

unicycler_check — long read assembly checker, aka the vibe check your assembly has been waiting for 💅

✨ SYNOPSIS ✨

unicycler_check [-h] --sam SAM --ref REF --reads READS [--min_len
MIN_LEN] [--error_window_size ERROR_WINDOW_SIZE] [--depth_window_size
DEPTH_WINDOW_SIZE] [--error_rate_threshold ERROR_RATE_THRESHOLD]
[--depth_p_val DEPTH_P_VAL] [--window_tables WINDOW_TABLES]
[--base_tables BASE_TABLES] [--html HTML] [--threads THREADS]
[--verbosity VERBOSITY]

like, three of those are mandatory and the rest are your little optional garnish 🎀

💜 DESCRIPTION 💜

Long read assembly checker.

periodt. that's the whole description, she's a woman of few words but MANY options. 😭

👑 OPTIONS 👑

okay here's the main event, the options, no skips, all of them, let's GO 🏃♀️💨

  • -h, --help — shows you this help message and then dips. classic. 🙈
  • --sam SAM — the input SAM file of alignments. and here's the lil plot twist: if that file doesn't exist yet, the alignment will actually be performed for you and the results saved to this file — you can use the aligner arguments with this script. so it's both the input and the output, main character energy fr fr 🔥
  • --ref REF — a FASTA file holding one or more reference sequences 🧬
  • --reads READS — a FASTQ file of long reads, the raw material, the moment ✨
  • --min_len MIN_LEN — minimum alignment length in bp. anything shorter than this gets excluded, sorry not sorry. (default: 100) 📏
  • --error_window_size ERROR_WINDOW_SIZE — the window size for error summaries. (default: 100) 🪟
  • --depth_window_size DEPTH_WINDOW_SIZE — the window size for depth summaries. (default: 100) 🌊
  • --error_rate_threshold ERROR_RATE_THRESHOLD — the threshold for high error rates, expressed as the fraction between the mean error rate and the random alignment error rate. (default: 0.3) 💀
  • --depth_p_val DEPTH_P_VAL — the p-value for low/high depth thresholds. (default: 0.001) 📊
  • --window_tables WINDOW_TABLES — path and/or prefix for table files summarising reference errors for reference windows. (default: do not save window tables) 📁
  • --base_tables BASE_TABLES — path and/or prefix for table files summarising reference errors at each base. (default: do not save base tables) 📁
  • --html HTML — path for the HTML report. (default: do not save HTML report) 🌈
  • --threads THREADS — number of CPU threads used to align. (default: the number of available CPUs) ⚡
  • --verbosity VERBOSITY — level of stdout information, from 0 to 2. (default: 1) 🗣️

🫶 SEE ALSO 🫶

unicycler(1) — go say hi to her sister, iykyk 💖

🎀 AUTHOR 🎀

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, we appreciate you, no cap 🫡💜

and that's the whole page bestie!! you read the entire thing, so proud of you 🥹🌸

ok one last lil sign-off: this is unicycler_check version 0.4.7, dated October 2018, and that's the whole vibe. slay, go check some assemblies, bye!! 💅✨🦋
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