Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps

St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or Io

A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.