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
currentGenomics Data Scientist, Weill Cornell MedicinecurrentGraduate Student, The Biophysical Sciences Program at the University of Chicago
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.
- Spearheaded the development of anvi'o snakemake workflows.
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.
Technical write-ups
Solutions or discussions regarding matters that are typically more technical than scientific.
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.
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.