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Improve and circularize single-genome assemblies and MAGs using Jorg - v1.0.0
kb_jorg

v.0.1.0

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Improve and circularize single-genome assemblies and MAGs from shotgun metagenomics data

Jorg is a tool to help improve or circularize genomes from shotgun metagenomics data.



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


This method assumes that you already have a pipeline that you like to use for assembling your metagenomes and creating bins.


Configuration:

Assembly Object: The Assembly object is a collection of assembled genome fragments, called "contigs".

Reads Object: The raw reads used to produce the original assembly and to be used for assembly improvement.

Read Mapping Tool: The read mapping tool used for coverage assessment and generation of the Circos diagram.

Kmer Length: Size of the kmers used during profiling (default: 33).

Minimum Coverage Value: Minimum coverage of the input genome required to run Jorg (default: 50).

Number of Iterations: Number of assembly and extension iterations to run using Jorg (default: 10).

High Contig Count Run: Check to make sure an input genome with many contigs is the truly intended input.

Output Assembly Selection Criteria: Select the criteria to decide which iteration output to use (default: Longest Single Fragment Assembly).

Minimum Overlap Length Required to Circularize: During check for circularization, indicate the overlap length to use (default: 100).


Output:

Output Object: The Assembly Object represents improved or cirularized assembly. This object can be used for downstream analysis.

Downloadable files: The relevant output of the Jorg run may be downloaded as a zip file. Contents include the clean sequence assembly files, last output, Jorg output files, and Circos input/output files.


Circos diagram description: inner-most black circle represent assembly contigs, mapped read are visualized in the red/grey/green colored outside ring where red is 0x-5x, grey is 5x-10x, and green is 10x-[Max Coverage Detected].


Related Publications


App Specification:

https://github.com/jungbluth/kb_jorg/tree/5e88c41a90fcef9e67a30fadebb3d4ee007b48eb/ui/narrative/methods/run_kb_jorg

Module Commit: 5e88c41a90fcef9e67a30fadebb3d4ee007b48eb