---
name: "shovill"
section: "1"
platform: "linux"
package: "shovill"
version: "1.1.0-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/shovill"
---

# shovill(1)

Assemble bacterial isolate genomes from Illumina paired-end reads

## NAME

shovill - Assemble bacterial isolate genomes from Illumina paired-end reads

## DESCRIPTION

SYNOPSIS

-

  De novo assembly pipeline for Illumina paired reads

USAGE

-

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

GENERAL

- **--help**

  This help

- **--version**

  Print version and exit

- **--check**

  Check dependencies are installed

INPUT

- **--R1** XXX

  Read 1 FASTQ (default: '')

- **--R2** XXX

  Read 2 FASTQ (default: '')

- **--depth** N

  Sub-sample **--R1**/--R2 to this depth. Disable with **--depth** 0 (default: 150)

- **--gsize** XXX

  Estimated genome size eg. 3.2M \<blank=AUTODETECT\> (default: '')

OUTPUT

- **--outdir** XXX

  Output folder (default: '')

- **--force**

  Force overwrite of existing output folder (default: OFF)

- **--minlen** N

  Minimum contig length \<0=AUTO\> (default: 0)

- **--mincov** n.nn

  Minimum contig coverage \<0=AUTO\> (default: 2)

- **--namefmt** XXX

  Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')

- **--keepfiles**

  Keep intermediate files (default: OFF)

RESOURCES

- **--tmpdir** XXX

  Fast temporary directory (default: '')

- **--cpus** N

  Number of CPUs to use (0=ALL) (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 \<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.