merenlab.org
Refining a bin using anvi'o – Meren Lab
http://merenlab.org/2015/05/11/anvi-refine
Refining a bin using anvi'o. A Murat Eren (Meren). Saving the refined group. As you know, hierarchical clustering in anvi’o (that is necessary to represent a merged dataset as a nice looking tree) requires the maximum number of splits to be around 20,000. If you have more, one way to do it is to profile your dataset with an. Value that eliminates enough short contigs from your analysis so you can merge everything without any issues. But what if you do not want to use a large. Many of your genome bins are...
merenlab.org
Removing contaminants from cultivars with anvi'o – Meren Lab
http://merenlab.org/2015/06/25/screening-cultivars
Removing contaminants from cultivars with anvi'o. Accessing genomic contamination levels is important, but not enough. Using anvi’o to screen for possible contaminants and to curate individual genomes. Example 1: axenic, uncontaminated culture. Example 2: non-axenic culture of 3 distinct bacterial populations. When Is a Microbial Culture Pure? Controlling for contamination in re-sequencing studies. Microbiome science threatened by contamination. By Connor Skennerton describe some key pitfalls. Using anvi...
merenlab.org
Combining metagenomics with metatranscriptomics – Meren Lab
http://merenlab.org/2015/06/10/combining-omics-data
Combining metagenomics with metatranscriptomics. A Murat Eren (Meren). Creating a precise clustering configuration. Calling interactive interface with the new clustering. The anvi’o metagenomics workflow. Is quite straighforward. But what if you have multiple sources of data that are mapped to the same contigs? If you have metagenomic, metatranscriptomic data from the same environment, and if you want to do a combined analysis, continue reading. And it is time to merge. Merging process creates multiple c...
merenlab.org
Analyzing single nucleotide variations (SNVs) with anvi'o – Meren Lab
http://merenlab.org/2015/07/20/analyzing-variability
Analyzing single nucleotide variations (SNVs) with anvi'o. A Murat Eren (Meren). This is more of a theoretical tutorial. For a more practical one on the same topic, please visit http:/ merenlab.org/tutorials/infant-gut/#profiling-snvs-in-a-bin. Characterization and reporting of SNVs. Generating a SNV profile. Parameters to filter the output. We use the term microbial clouds. Makes it somewhat irrelevant to microbiology). The heterogeneity of the microbial cloud,. And/or the stringency of mapping. Charact...
merenlab.org
Comparing different mapping software using anvi'o – Meren Lab
http://merenlab.org/2015/06/23/comparing-different-mapping-software
Comparing different mapping software using anvi'o. A Murat Eren (Meren). A quick first look and initial binning. Number of mapped reads by each mapper. Comparing individual mapping results. Putting all mapping results together. During our discussions to identify which mapping software should we use to map short metagenomic reads to contigs, Bing Ma. But beyond our preliminary findings on the performance of these mapping software, this little project gives a good idea about how versatile anvi’o. HUZ63 is ...
merenlab.org
An analysis and visualization platform for 'omics data – Meren Lab
http://merenlab.org/projects/anvio
Anvi’o in a nutshell. Anvi’o is an analysis and visualization platform for ‘omics data. It brings together many aspects of today’s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs. Please see the Tutorials. Pull-down menu on this page for some example workflows with anvi’o. Anvi’o is a community-driven, GPL-licensed open-source project. You can browse its codebase by clicking here. And you can find our methods paper for anvi’o by clicking here.
merenlab.org
Installing anvi'o – Meren Lab
http://merenlab.org/2015/05/01/installation
An overview of anvi’o dependencies. Installing the latest stable release (safe mode). Installing or updating from the current codebase (semi-pro). Installation for developers (you’re a wizard, arry). Running the Mini Test. The latest version of anvi’o is 2.0.2. See the release notes. This article explains basic steps of installing anvi’o using rather conventional methods. There are other installation options for OS X. Users, and Docker. For more technical problems. An overview of anvi’o dependencies.
