contigs
GraphBin: Refined binning of metagenomic contigs using assembly graphs.
Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.
Pandoo: a pipeline of tools for bacterial genomics.
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
PlasFlow - predicting plasmid sequences in metagenomic data
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