New ERGO Feature: Metagenome Analysis

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Easily analyze your metagenome projects using ERGO by dragging and dropping your BIOM file into ERGO. The BIOM format is the standard interchange format for Metagenome experiments. You can find more information here: http://biom-format.org/index.html. After your BIOM file has been imported into ERGO, it analyzes it and computes some metrics such as total number of otus per sample, the Top 20 OTUs in all samples, and more. You can find this information on the “Overview” tab.

Now that your BIOM file is in ERGO, you can compute the Principal Coordinates Analysis (PCoA) or Richness Estimates, or a Taxonomic Bar Chart. All of these options are available to you by a click of a button. These analysis are made available by using the wonderful open source software we’ve integrated into ERGO: R, phyloseq and vegan. These packages have been cited thousands of times and are the standard for ecological/metagenome studies. However, using R and these software can be challenging. This is why ERGO exists: to make the best tools available to all researchers.

For PCoA and Richness estimates, ERGO will compute Analysis of Similarities (ANOSIM) to test the significance of group differences. For example, the box plot below is from a study of microbiomes of different body sites in homo sapiens. The Y-Axis of the plot the Shannon Index, a measurement of species richness and evenness. The X-Axis is the groups of samples that are from different body sites. ERGO helpfully provides the significance of the group difference via ANOSIM to be P = 0.002**.

If you’d like to learn more about metagenome/microbiome analysis in ERGO, please feel free to reach out using the form below.

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New ERGO Feature: Affected Features for Variants

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When you add annotated BCF or VCF files to ERGO, it automatically computes variant metrics, including the features that have been affected. Easily find which genomic features are affected by variation by clicking on the “Affected Features” tab. From here you can search for your feature or function of interest and see which features have been affected. Clicking on the arrow reveals more information about the feature, including which pathways it is in and which variants have affected this feature.

New ERGO Feature: Variant Filtering

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Hey ERGO users! You can now filter through the large lists of variants according to their fields and focus in on the ones that are most important. The variant filtering feature can be found under the “Variant List” tab in the variant analysis workflow. By simply clicking on “Add Filter”, located next to “Settings”, you can choose your filter(s) and focus in on specific contigs, frame shifts, specific annotations and attributes, and much more.