stenglein-lab/2022_Annual_Review_of_Virology

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stenglein-lab/2022_Annual_Review_of_Virology

stenglein-lab

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This repository contains code used to perform analyses described in a 2022 Annual Review of Virology review article.

viral_variant_caller

A nextflow pipeline to call single nucleotide and structural variants in viral populations

stenglein_lab_scripts

Stenglein Lab Scripts

taxonomy_pipeline

A nextflow pipeline to taxonomically assess the sequences in an NGS dataset, with a focus on identifying and characterizing virus sequences

2017_GDW

Documents and exercises used in the Genomics of Disease in Wildlife Workshop June 2017

tick_surveillance

Bioinformatics pipeline for analysis of amplicon sequencing of tick-associated microbes

bunya_dvg_analyses

Analyses of DVG forms in ~100 bunyavirus datasets

highlight_residues_on_spike_structure

Highlight structures on SARS-CoV-2 spike structure using UCSF chimera

nextflow_template

A simple nextflow template - can be forked to initiate a new nextflow workflow

MIP_280A4_Fall_2021

Course Material for MIP_280A4, Computational Microbiology, for Fall 2021

active_learning_exercises

These are mostly paper-based active learning exercises developed to teach computational biology concepts in courses and workshops.

2022_Todos_Santos

Training material from the 2022 Todos Santos Genomics and Bioinformatics workshop.

lab_freezer_monitor

Simple lab freezer monitor using raspberry pis and a web interface

btv_segment_table

A pipeline to quantify #s of reads mapping to bluetongue virus (BTV) segments in a co-infection/reassortment experiment