Metagenomic Binning Service

Overview

The Metagenomic Binning Service accepts either reads or contigs, and attempts to “bin” the data into a set of genomes. This service can be used to reconstruct bacterial and archael genomes from environmental samples.

Using the Metagenomic Binning Service

The Metagenomic Binning submenu option under the Services main menu (Genomics category) opens the Metagenomic Binning Service input form (shown below). Note: You must be logged into PATRIC to use this service.

../../_images/services_menu.pngMetagenomic Binning Menu

Options

../../_images/metagenome_binning_input_form.pngMetagenomic Binning Input Form

Paired read library

Read File 1 & 2

Many paired read libraries are given as file pairs, with each file containing half of each read pair. Paired read files are expected to be sorted such that each read in a pair occurs in the same Nth position as its mate in their respective files. These files are specified as READ FILE 1 and READ FILE 2. For a given file pair, the selection of which file is READ 1 and which is READ 2 does not matter.

Contigs

Alternatively, contigs can be used with the service instead of read files.

Parameters

Output Folder

The workspace folder where results will be placed.

Output Name

Name used to uniquely identify results.

Genome Group Name

Name used to create genome group with identified genomes.

Output Results

../../_images/metagenomic_binning_result.pngMetagenomic Binning Service Output Files

The Metagenomic Binning Service generates several files that are deposited in the Private Workspace in the designated Output Folder. These include

  • BinningReport.html - Document containing the list of bins and other summary information. Double-clicking on this file to display it. ../../_images/metagenomic_binning_report.pngMetagenomic Binning Report
  • bin.#.#### - Annotation job result of bin number #.
  • bin.#.####.fa - a FASTA file containing the bin’s contigs for bin number #.