Follow up to Grace Blackwell's 661k dataset, for 2023

Bioinformatics program inStrain

MAGinator - Accurate SNV calling and profiling of MAGs

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

Pipeline used to generate data on spire.embl.de

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

Bacterial GWAS analysis

Build a map of genes present across a set of microbial genomes

Prophage-DB scripts for generating figures

Discover and annotate the virome

sensitive and precise assembly of short sequencing reads

MetagenOmic read Re-Assigner and abundance quantifier

Read coverage calculator for metagenomics

Novelty-inclusive microbial community profiling of shotgun metagenomes

Computation of average nucleotide identity with the use of MMseqs2

Experimental features for Nextflow

Logan Unitigs and Contigs

Workflow to assign Taxonomy to a bacteriophage genome isolate

Genomic language model predicts protein co-regulation and function

Fast and Accurate Variant Identification Tool for Sequencing-Based Studies

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes

PLMSearch enables accurate and fast homologous protein search with only sequences as input

GPT4All: Run Local LLMs on Any Device. Open-source and available for commercial use.

skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Panel: The powerful data exploration & web app framework for Python

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

Strain-level haplotyping for metagenomes with short or long-reads.