MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates

Curated publicly available genomic data of fermented foods + microbes

A BLAST-based program for analyzing Average Nucleotide Identity

A list of software for pangenomics

A fast Rust based tool to serialize text-based files in a repository or directory for LLM consumption

Genomic Pre-trained Network

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

🍄 Qiime2 ITS classifiers for the UNITE database

A gap-closing software tool that uses long reads to enhance genome assembly.

Rapid and simple taxonomic profiling of genome and metagenome contigs

A tool to create visual HTML reports from collections of CSV/TSV tables

Oxford Nanopore's Basecaller

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Snakemake+python workflow to highly parallelize variant calling in non-model organisms

toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Nanopore data assembler

Neural network classification of TE

A command-line podcast aggregator

Open source code for AlphaFold 2.

An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.

Bacterial Annotation by Learned Representation of Genes

use paired-end transcriptome reads to scaffold genomes

Python utilities for Manubot: Manuscripts, open and automated

This is the Haplotypo repository

This is a singularity container designed to be a portable and complete funannotate black box.

Applied Computational Genomics Course at UU: Spring 2020