UNICYCLER(1)

💖 UNICYCLER(1) — the unicycler manual page, but make it a group chat 💖

okay bestie, gather round, because today we're learning about unicycler from the User Commands section of the manual. yes it's a Unix tool, yes it's about assembling bacterial genomes, yes it's giving main character energy. let's go 🧬✨

🌸 NAME 🌸

unicycler — assembly pipeline for bacterial genomes. that's it, that's the whole name. short. iconic. periodt. 💅

✨ SYNOPSIS ✨

unicycler [-h] [--help_all] [--version] [-1 SHORT1] [-2 SHORT2] [-s
UNPAIRED] [-l LONG] -o OUT [--verbosity VERBOSITY] [--min_fasta_length
MIN_FASTA_LENGTH] [--keep KEEP] [-t THREADS] [--mode
{conservative,normal,bold}] [--linear_seqs LINEAR_SEQS] [--vcf]

like, look at all those flags. she's flexible. she's got range. 🎀

🦋 DESCRIPTION 🦋

okay so unicycler is an assembly pipeline for bacterial genomes — and no cap, it's lowkey a triple threat because it can do three different vibes depending on what you feed it. 🌈

• got only Illumina reads? she acts as a SPAdes-optimiser. slay.
• got only long reads (PacBio or Nanopore)? she runs a miniasm+Racon pipeline. ate.
• want the best possible assemblies? give her both Illumina reads and long reads and she'll conduct a hybrid assembly. that's the dream combo, fr fr. 💖

👑 OPTIONS 👑

the basics 💫

• -h, --help — shows this help message and then dips. exit stage left. ✌️
• --help_all — shows a help message with all the program options. the full lore, not just the trailer. 📖
• --version — shows Unicycler's version number. identity check. 🪪

✨ Input ✨

• -1 SHORT1, --short1 SHORT1 — FASTQ file of the first short reads in each pair. required, bestie, you cannot skip this one. 🚨
• -2 SHORT2, --short2 SHORT2 — FASTQ file of the second short reads in each pair. also required. the pair is the point. 👯
• -s UNPAIRED, --unpaired UNPAIRED — FASTQ file of unpaired short reads. optional — she's the single friend tagging along, and she's welcome. 🫶
• -l LONG, --long LONG — FASTQ or FASTA file of long reads. optional. the long reads. the drama. the range. 🐍

🌸 Output 🌸

• -o OUT, --out OUT — output directory. required! she needs somewhere to put all her little files. 🏠
• --verbosity VERBOSITY — level of stdout and log file information. default is 1. pick your chatter level:
  • 0 = no stdout, silent treatment 💀
  • 1 = basic progress indicators
  • 2 = extra info
  • 3 = debugging info
• --min_fasta_length MIN_FASTA_LENGTH — excludes contigs from the FASTA file which are shorter than this length. default is 100. tiny contigs, get out of my house. 🚪
• --keep KEEP — level of file retention. default is 1. how much stuff do you want to keep around:
  • 0 = only keep final files: assembly (FASTA,GFA and log)
  • 1 = also save graphs at main checkpoints
  • 2 = also keep SAM (enables fast rerun in different mode)
  • 3 = keep all temp files and save all graphs (for debugging)
• --vcf — produce a VCF by mapping the short reads to the final assembly. experimental, and the default is: do not produce a vcf file. so if you want the vcf you have to ask for the vcf. 🧪

⭐ Other ⭐

• -t THREADS, --threads THREADS — number of threads used. default is 4. give her more threads, she'll go faster, she's got the stamina. 🔥
• --mode {conservative,normal,bold} — bridging mode. default is normal. choose your fighter:
  • conservative = smaller contigs, lowest misassembly rate — the careful queen 🎀
  • normal = moderate contig size and misassembly rate — the balanced icon ⚖️
  • bold = longest contigs, higher misassembly rate — go big or go home 💅
• --linear_seqs LINEAR_SEQS — the expected number of linear (i.e. non-circular) sequences in the underlying sequence. default is 0. circles are the default assumption, bestie. 🔵

💜 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 absolute legend, we appreciate you 🫶

and that's the whole page, no crumbs left. 💖 this was unicycler version 0.4.7, dated October 2018 — so yeah, she's a 2018 girlie, but she still runs the game. go assemble something gorgeous, bestie. 🦋✨👑