SHOVILL(1)

📦 version 1.1.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SHOVILL 💖

okay bestie, welcome to the shovill manual page, manual section 1, filed under User Commands. if you've got a bacterial isolate, some Illumina paired-end reads, and a dream, this is literally the page for you. pull up a chair. 🫶

✨ NAME ✨

shovill — assemble bacterial isolate genomes from Illumina paired-end reads

🌸 DESCRIPTION 🌸

💅 SYNOPSIS

de novo assembly pipeline for Illumina paired reads. that's it, that's the whole vibe.

🎀 USAGE

shovill [options] --outdir DIR --R1 R1.fq.gz --R2 R2.fq.gz

⭐ GENERAL

  • --help — prints this help. the classic. the icon. 👑
  • --version — print the version and dip. exits right after, no small talk.
  • --check — check that your dependencies are actually installed, so you don't get jumpscared halfway through a run. 💀

🧚 INPUT

  • --R1 XXX — read 1 FASTQ (default: '')
  • --R2 XXX — read 2 FASTQ (default: '')
  • --depth N — sub-sample --R1/--R2 down to this depth. want it off? disable it with --depth 0 (default: 150)
  • --gsize XXX — estimated genome size, eg. 3.2M. leave it blank and it's <blank=AUTODETECT> (default: '')

🍓 OUTPUT

  • --outdir XXX — output folder (default: '')
  • --force — force overwrite of an existing output folder (default: OFF). yeah she will absolutely clobber it, so be sure bestie 🫣
  • --minlen N — minimum contig length, where <0=AUTO> (default: 0)
  • --mincov n.nn — minimum contig coverage, where <0=AUTO> (default: 2)
  • --namefmt XXX — format of the contig FASTA IDs, in printf style (default: 'contig%05d')
  • --keepfiles — keep the intermediate files (default: OFF). for when you're nosy about what happened in the middle 💅

🦋 RESOURCES

  • --tmpdir XXX — fast temporary directory (default: '')
  • --cpus N — number of CPUs to use, and 0=ALL if you're feeling greedy (default: 8)
  • --ram n.nn — try to keep RAM usage below this many GB (default: 7.54)

🔥 ASSEMBLER

  • --assembler XXX — assembler: velvet spades skesa megahit (default: 'spades')
  • --opts XXX — extra assembler options, in quotes, eg. spades: '--sc' (default: '')
  • --kmers XXX — k-mers to use, where <blank=AUTO> (default: '')

🌈 MODULES

  • --trim — enable adaptor trimming (default: OFF)
  • --noreadcorr — disable read error correction (default: OFF)
  • --nostitch — disable read stitching (default: OFF)
  • --nocorr — disable post-assembly correction (default: OFF)

👑 HOMEPAGE

https://github.com/tseemann/shovill — Torsten Seemann

💜 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, no cap ✨

this was shovill version 1.1.0, dated June 2020, living in manual section 1 as SHOVILL(1). go assemble something iconic. periodt 💅💖

📦 where this page comes from