Bilingual Language Model for Protein Sequence and Structure

A flexible pipeline for complete analysis of bacterial genomes

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

A pairwise sequence aligner written in Rust

Phage Annotation using Protein Structures

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

A fast approximate aligner for long DNA sequences

Reorients assembled microbial sequences

fast phage annotation program

A Nextflow full-length 16S profiling pipeline for ONT reads

MEGAN Community Edition

🚀 R package: future: Unified Parallel and Distributed Processing in R for Everyone

Nextflow pipeline for plasmid detection and classification from metagenomic data

WtP: Phage identification via nextflow and docker or singularity

Analyzing sketching and sampling approaches for fast and accurate read classification

🚥 Visualizing publication-quality multiple sequence alignment using ggplot2

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

SPAdes Genome Assembler

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

A 21 century R console

A versatile pairwise aligner for genomic and spliced nucleotide sequences

ARTIC SARS-CoV-2 workflow and reporting

All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis

💔 An implementation of scale functions for setting axis breaks of a 'gg' plot.

A grammar of graphics for comparative genomics

Software for generating Metagenomic samples of realistic Microbial Mock communities

Repository for suggesting new lineages that should be added to the current scheme

minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

This package contains deep learning models and related scripts for RoseTTAFold

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.