A. Murat Eren (Meren) of anvi'o


Computer scientist and microbial ecologist interested in undersatnding mechanisms by which microbes interact with their surroundings, evolve, disperse, and respond to environmental change.


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Program contributions

anvi-cluster-contigs anvi-compute-completeness anvi-compute-functional-enrichment-in-pan anvi-db-info anvi-delete-collection anvi-delete-functions anvi-delete-hmms anvi-delete-misc-data anvi-delete-state anvi-display-functions anvi-display-pan anvi-estimate-genome-completeness anvi-estimate-scg-taxonomy anvi-estimate-trna-taxonomy anvi-experimental-organization anvi-export-collection anvi-export-contigs anvi-export-functions anvi-export-gene-calls anvi-export-gene-coverage-and-detection anvi-export-items-order anvi-export-misc-data anvi-export-splits-and-coverages anvi-export-splits-taxonomy anvi-export-state anvi-gen-contigs-database anvi-gen-gene-consensus-sequences anvi-gen-gene-level-stats-databases anvi-gen-genomes-storage anvi-gen-phylogenomic-tree anvi-gen-variability-network anvi-gen-variability-profile anvi-get-aa-counts anvi-get-codon-frequencies anvi-get-sequences-for-gene-calls anvi-get-sequences-for-gene-clusters anvi-get-sequences-for-hmm-hits anvi-get-short-reads-from-bam anvi-get-short-reads-mapping-to-a-gene anvi-get-split-coverages anvi-get-tlen-dist-from-bam anvi-import-collection anvi-import-functions anvi-import-items-order anvi-import-misc-data anvi-import-state anvi-import-taxonomy-for-genes anvi-import-taxonomy-for-layers anvi-init-bam anvi-interactive anvi-matrix-to-newick anvi-merge anvi-merge-bins anvi-meta-pan-genome anvi-migrate anvi-oligotype-linkmers anvi-pan-genome anvi-profile anvi-profile-blitz anvi-refine anvi-rename-bins anvi-report-inversions anvi-report-linkmers anvi-run-hmms anvi-run-ncbi-cogs anvi-run-scg-taxonomy anvi-run-trna-taxonomy anvi-scan-trnas anvi-search-functions anvi-search-palindromes anvi-search-primers anvi-search-sequence-motifs anvi-setup-ncbi-cogs anvi-setup-scg-taxonomy anvi-setup-trna-taxonomy anvi-show-collections-and-bins anvi-show-misc-data anvi-split anvi-summarize anvi-update-db-description anvi-script-add-default-collection anvi-script-as-markdown anvi-script-augustus-output-to-external-gene-calls anvi-script-compute-ani-for-fasta anvi-script-estimate-metabolic-independence anvi-script-filter-fasta-by-blast anvi-script-fix-homopolymer-indels anvi-script-gen-distribution-of-genes-in-a-bin anvi-script-gen-function-matrix-across-genomes anvi-script-gen-functions-per-group-stats-output anvi-script-gen-hmm-hits-matrix-across-genomes anvi-script-gen-short-reads anvi-script-gen_stats_for_single_copy_genes.py anvi-script-get-hmm-hits-per-gene-call anvi-script-merge-collections anvi-script-pfam-accessions-to-hmms-directory anvi-script-process-genbank-metadata anvi-script-reformat-fasta anvi-script-snvs-to-interactive anvi-script-transpose-matrix

Resource contributions

Tutorials and exercises

Kinds of write-ups that typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi'o often with hands-on experience.

Basics of metagenomic read recruitment A very simple introduction to metagenomic read recruitment.
A metagenomic read recruitment exercise A mini hands-on exercise is to conduct a simple read recruitment experiment with a mock dataset.
A pangenomics exercise A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course.
Anvi'o phylogenomics workflow A comprehensive description of the anvi'o phylogenomics workflow.
Anvi'o tools for microbial population genetics A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output.
A primer on anvi'o with the Infant Gut Dataset A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.

Technical write-ups

Solutions or discussions regarding matters that are typically more technical than scientific.

Anvi'o interactive interface 101 A short tutorial that walks you through the capabilities of the anvi'o interactive interface using an intuitive dataset and _without_ using any of the actual anvi'o functionality.
Data types of anvi'o interactive interface a more detailed description of the interface by demonstrating the data types the interface can work with, and later details of the user interface.
Combining multiple 'omics data types A workflow that describes how to combine metagenomics and metatrasncriptomics data appropriately.
Accessing and including NCBI genomes in 'omics analyses in anvi'o A tutorial that will walk you through the steps of downloading genomes of interest from the NCBI, processing NCBI GenBank files to get anvi’o compatible files, and running the anvi’o snakemake workflow for contigs to generate a contigs database for each of these genomes.

Articles, workflows, opinions

Key insights into specific topics and can be useful to more advanced users and 'omics enthusiasts in general.

Visualizing the fate of contigs across metagenomic binning algorithms A visual demonstration of the shortcomings of automatic binning of genomes from complex environments using short-read assemblies.