shovill | CPG Portal

shovillShovill is a bacterial isolate genome assembly pipeline for Illumina paired-end reads. It uses SPAdes at its core but alters the pre- and post-processing steps to produce similar assemblies in less time. Also supports SKESA, Velvet, and Megahit as alternative assemblers. Performs genome size estimation, read subsampling (default 150x), adapter trimming, read error correction, read stitching, assembly, post-assembly correction, and contig filtering by length, coverage, and homopolymers.Versions

v1.4.2 (default)

Tags: genome assembly, bacterial genomics, Illumina, SPAdes, cpgParameters

R1 (file) required: Read 1 FASTQ file (paired-end)

R2 (file) required: Read 2 FASTQ file (paired-end)

depth (int): Sub-sample reads to this depth. Disable with 0 (default: 150)

gsize (str): Estimated genome size (e.g. 3.2M). If blank, auto-detected via mash

assembler (enum): Assembler to use for the primary assembly step. Options: spades, skesa, velvet, megahit

plasmid (bool): Enable plasmid mode (SPAdes only)

trim (bool): Enable adaptor trimming with Trimmomatic

noreadcorr (bool): Disable read error correction

nostitch (bool): Disable read stitching/overlap

nocorr (bool): Disable post-assembly correction

Links

GitHub repository

License: GPL-2.0

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