A tool for generating consensus long-read assemblies for bacterial genomes

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

Stay Focused. Take a Break.

Multiple Protein Structure Alignment at Scale with FoldMason

A tool for removing redundant genomes from a set of assemblies

in silico typing of the H. influenzae cap locus

Slices/subsections genbank files by either gene names, locus tags or base pair range. Handles multi-genbank files

De novo assembler for single molecule sequencing reads using repeat graphs

hybrid assembly pipeline for bacterial genomes

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Split Kmer Analysis

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

Order and orientation of complete bacterial genomes

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Extract alleles from genome assemblies

The second version of the Kraken taxonomic sequence classification system

Unaffiliated fork off https://linksawakeningdxhd.itch.io/links-awakening-dx-hd

CarveMe: genome-scale metabolic model reconstruction

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

Analyzing and visualizing KEGG information using the grammar of graphics

Bifrost graph gene caller.

MMseqs2: ultra fast and sensitive search and clustering suite

Kaptive web interface

bacterial read typer 🧬 🛹 🦠

a tool for counting dead ends in GFA assembly graphs

ONT-first assembly pipeline