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Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.2
kb_das_tool

v.1.0.3

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Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.



Implemented for KBase by Sean Jungbluth(sjungbluth@lbl.gov)


DAS Tool takes metagenome "bins" generated from the same assembly, but using different genome binning tools, and optimizes their content using a dereplication, aggregation and scoring strategy.


Configuration:

Assembly Object: The Assembly object is a collection of assembled genome fragments, called "contigs". These are part of the input file required for DAS Tool to run. Currently only a single Assembly object is accepted by the DAS Tool App.

Input BinnedContig Object Names: The BinnedContig Objects represents the different genome binning tool output binned contigs to be used for input to DAS Tool.

Output BinnedContig Object Name: The output BinnedContig Object is produced by DAS Tool.


Output:

Output Object:The BinnedContig Object represents the directory of binned contigs created by DAS Tool. This object can be used for downstream analysis.

Output Bin Summary Report:The number of bins produced, the number of contigs that were binned and the total number of contigs in the assembly.

Downloadable files: The enitre output of the DAS Tool run may be downloaded as a zip file.

Related Publications


App Specification:

https://github.com/jungbluth/kb_das_tool/tree/1e22b36fe34fc1afcb6857b56c1d8c2aa022db57/ui/narrative/methods/run_kb_das_tool

Module Commit: 1e22b36fe34fc1afcb6857b56c1d8c2aa022db57