shovill - Assemble bacterial isolate genomes from Illumina paired-end reads

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

shovill 1.1.0                                       June 2020                                         SHOVILL(1)

       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

       shovill - Assemble bacterial isolate genomes from Illumina paired-end reads