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.