krabberod

vsearch

Versatile open-source tool for microbiome analysis

audiocraft

Audiocraft is a library for audio processing and generation with deep learning. It features the state-of-the-art EnCodec audio compressor / tokenizer, along with MusicGen, a simple and controllable music generation LM with textual and melodic conditioning.

sv-genotyping

Benchmarking structural variant genotyping

mapping-benchmarking

Snakemake pipeline for benchmarking read mappers

genome-assembly-workshop-2023

long-reads

Data and scripts for "Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity" (Jamy et al. 2019)

vg

tools for working with genome variation graphs

PTP

PTP model for species delimitation

cue

Deep learning framework for SV calling and genotyping

pbsv

pbsv - PacBio structural variant (SV) calling and analysis tools

svim

Structural Variant Identification Method using Long Reads

samplot

Plot structural variant signals from many BAMs and CRAMs

syri

Synteny and Rearrangement Identifier

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Pirate-MIDI-BridgeOS

Documenting Bugs & Issues - Public Collaboration

Arabidopsis_assemblies

De novo assembly and annotation of the Arabidopsis arenosa genome reveal local gene duplication in the MADS-box type I family

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

pr2database

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

CodeJam

Google code jam practice answers

gggenomes

A grammar of graphics for comparative genomics

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

r-color-palettes

Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜

docs.nextstrain.org

Umbrella documentation project for Nextstrain

hpc

Wiki for the CEES HPC resources

hifiasm-meta

hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.

Module-1-Unix-Python

wesanderson

A Wes Anderson color palette for R

lulu

r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)

tensorflow-wavenet

A TensorFlow implementation of DeepMind's WaveNet paper

SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data