UNICYCLER_ALIGN(1)

👑 UNICYCLER_ALIGN(1) — user commands, bestie 💅

okay so this is the manual page for unicycler_align, and it lives in section 1 of the manual (that's the user-commands girlies 🫶). Strap in, it's giving "long reads but make it aligned" and honestly? obsessed.

✨ NAME ✨

unicycler_align — the sensitive semi-global long read aligner 🌸 like it literally takes your long reads and lines them up against your reference with feelings and precision. sensitive queen behavior, no cap.

🦋 SYNOPSIS 🦋

unicycler_align [-h] --ref REF --reads READS --sam SAM [--contamination
CONTAMINATION] [--scores SCORES] [--low_score LOW_SCORE] [--keep_bad]
[--sensitivity SENSITIVITY] [--threads THREADS] [--verbosity VERBOSITY]
[--min_len MIN_LEN] [--allowed_overlap ALLOWED_OVERLAP]

like… it's a lot of brackets but that's just the options being optional, ok?? --ref, --reads and --sam are the main characters and they are NOT optional. periodt. 💖

🌈 DESCRIPTION 🌈

Unicycler align — a sensitive semi-global long read aligner 💫 that's it, that's the whole vibe. it aligns long reads. sensitively. semi-globally. iconic.

🎀 OPTIONS 🎀

• -h, --help — shows you this help message and then dips out. exit stage left, thank u next 👋
• --ref REF — a FASTA file holding one or more reference sequences. this is the thing you're aligning to, the main character of the whole operation ngl 🧚
• --reads READS — a FASTQ or FASTA file of long reads. yes bestie, either format, she's flexible 💅
• --sam SAM — the SAM file where all the resulting alignments go. this is the receipts file, the ✨output✨
• --contamination CONTAMINATION — a FASTA file of known contamination lurking in your long reads 🦠 get it outta here
• --scores SCORES — a comma-delimited string of alignment scores, in this exact order: match, mismatch, gap open, gap extend. (default: 3,-6,-5,-2) 🔥 do not shuffle the order, she will know.
• --low_score LOW_SCORE — score threshold, and alignments below it are considered poor 😭 (default: the threshold gets set automatically, she's smart like that)
• --keep_bad — includes alignments in the results even when they're below the low score threshold. (default: low-scoring alignments get discarded 🗑️) so like, by default she's ruthless and only keeps the good ones, but this flag says "no babe keep them all, I want the messy ones too"
• --sensitivity SENSITIVITY — a number from 0 (least sensitive) to 3 (most sensitive) (default: 0) 🌸 crank it up if you want her to try harder
• --threads THREADS — number of threads used (default: number of CPUs, up to 8) ⚡ she'll use as many cores as you've got, but only up to 8, she has boundaries
• --verbosity VERBOSITY — level of stdout information, from 0 to 4 (default: 1) 👀 how chatty she is in your terminal
• --min_len MIN_LEN — minimum alignment length in bp, and alignments shorter than this get excluded (default: 100) 📏 short alignments are simply not invited
• --allowed_overlap ALLOWED_OVERLAP — allow this much overlap between alignments within a single read (default: 100) 🫶 a lil overlap is fine, it's a cuddle not a crime

💜 SEE ALSO 💜

• unicycler(1) — go say hi to her big 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, you ate that fr fr 👑

okay that's the whole page bestie, go align something gorgeous 💫

signing off with all the specs: unicycler_align version 0.4.7, dated October 2018 🎀✨ mwah, no cap 💅