shovill - Assemble bacterial isolate genomes from Illumina
paired-end reads
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
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.