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.