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.