.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
.TH SHOVILL "1" "June 2020" "shovill 1.1.0" "User Commands"
.SH NAME
shovill \- Assemble bacterial isolate genomes from Illumina paired-end reads
.SH DESCRIPTION
SYNOPSIS
.IP
De novo assembly pipeline for Illumina paired reads
.PP
USAGE
.IP
shovill [options] \fB\-\-outdir\fR DIR \fB\-\-R1\fR R1.fq.gz \fB\-\-R2\fR R2.fq.gz
.PP
GENERAL
.TP
\fB\-\-help\fR
This help
.TP
\fB\-\-version\fR
Print version and exit
.TP
\fB\-\-check\fR
Check dependencies are installed
.PP
INPUT
.TP
\fB\-\-R1\fR XXX
Read 1 FASTQ (default: '')
.TP
\fB\-\-R2\fR XXX
Read 2 FASTQ (default: '')
.TP
\fB\-\-depth\fR N
Sub\-sample \fB\-\-R1\fR/\-\-R2 to this depth. Disable with \fB\-\-depth\fR 0 (default: 150)
.TP
\fB\-\-gsize\fR XXX
Estimated genome size eg. 3.2M <blank=AUTODETECT> (default: '')
.PP
OUTPUT
.TP
\fB\-\-outdir\fR XXX
Output folder (default: '')
.TP
\fB\-\-force\fR
Force overwrite of existing output folder (default: OFF)
.TP
\fB\-\-minlen\fR N
Minimum contig length <0=AUTO> (default: 0)
.TP
\fB\-\-mincov\fR n.nn
Minimum contig coverage <0=AUTO> (default: 2)
.TP
\fB\-\-namefmt\fR XXX
Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')
.TP
\fB\-\-keepfiles\fR
Keep intermediate files (default: OFF)
.PP
RESOURCES
.TP
\fB\-\-tmpdir\fR XXX
Fast temporary directory (default: '')
.TP
\fB\-\-cpus\fR N
Number of CPUs to use (0=ALL) (default: 8)
.TP
\fB\-\-ram\fR n.nn
Try to keep RAM usage below this many GB (default: 7.54)
.PP
ASSEMBLER
.HP
\fB\-\-assembler\fR XXX Assembler: velvet spades skesa megahit (default: 'spades')
.TP
\fB\-\-opts\fR XXX
Extra assembler options in quotes eg. spades: '\-\-sc' (default: '')
.TP
\fB\-\-kmers\fR XXX
K\-mers to use <blank=AUTO> (default: '')
.PP
MODULES
.TP
\fB\-\-trim\fR
Enable adaptor trimming (default: OFF)
.TP
\fB\-\-noreadcorr\fR
Disable read error correction (default: OFF)
.TP
\fB\-\-nostitch\fR
Disable read stitching (default: OFF)
.TP
\fB\-\-nocorr\fR
Disable post\-assembly correction (default: OFF)
.PP
HOMEPAGE
.IP
https://github.com/tseemann/shovill \- Torsten Seemann
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.