Alon Shaiber of anvi'o

Bio

Computational scientist previously studying microbial ecology, currently studying structural variation in cancer genomics, and what's next? Who knows?

Affiliations

Contact info or affiliations needs an update? Edit these files.

Intellectual contributions

Some contributions are more than code. Inevitably, this manually curated list will be incomplete for almost everyone, but nevertheless, we try to keep track of key contributions made by memebers of the anvi'o commmunity to the platform and its users. Edit these files to help.

Program contributions

anvi-export-locus anvi-gen-variability-profile anvi-run-workflow

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.

The anvi'o pangenomics workflow A comprehensive description of the anvi'o pangenomics workflow.
pangenomics theoretical beginner

Technical write-ups

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

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.
pangenomics hands-on intermediate
Extract loci from genomes and metagenomes with anvi'o A tutorial on how to use anvi-export-locus to target genomic regions of interest across genomes and/or metagenomic assemblies, and report sequences and/or anvi’o contigs databases for cut loci for downstream analyses.
genomics hands-on intermediate