Pandoo: a pipeline of tools for bacterial genomics.
GraphBin: Refined binning of metagenomic contigs using assembly graphs.
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
PlasFlow - predicting plasmid sequences in metagenomic data
