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appliedgenomics2021

Materials for Spring 2021 Applied Genomics Course

bangui_bunyavirus

Data and R code used in Orf et al. (2023) "Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans." https://doi.org/10.1093/ve/vead018

covseq

CoV-Seq: COVID-19 Genomic Sequence Database and Visualization

dge_workshop

exonerate_active_pseudo

exonerate_for_transposon_annotation

fieldbioinformatics

The ARTIC field bioinformatics pipeline

freyja

Depth-weighted De-Mixing

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

mgescan

A Galaxy based system for identifying retrotransposons in genome

monkeypox-genome-assembly

Genome assembly pipelines for next- and thrid-generation sequencing datasets

mpox-dynamics

mscaffolder

A comparative genome scaffolding tool

pangolearn

Store of the trained model for pangolin to access.

paper-zhang2014

pingpongpro

Find ping-pong signatures in piRNA-Seq data like a pro

porecov

SARS-CoV-2 workflow for nanopore sequence data

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

sars-cov-2

SARs-CoV-2 Primer schemes

skyline-plots

Inference of past population dynamics using Bayesian Coalescent Skyline and Birth-Death Skyline plots.

streptococcus_suis

Principal components analysis of SNPs of Streptococcus suis

traitmodels-wme

Tutorials for working with trees in R

transposons

Drosophila transposable element consensus sequences

v-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

variationtoolkit

Automatically exported from code.google.com/p/variationtoolkit