Genome browser and variant annotation

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Phage Annotation using Protein Structures

Python package for detection of chimerism and contamination in prokaryotic genomes.

Visualise and analyse nanopore (ONT) raw signals

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

genomic variant frequency estimation

♥ Efficient Estimation of Evolutionary Distances

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

Synteny and Rearrangement Identifier

Automatically exported from code.google.com/p/cdhit

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing

Randomly subsample sequencing reads or alignments

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

Correcting errors in noisy long reads using variation graphs

🚀 A sequencing simulator

Reorients assembled microbial sequences

Langevin dynamics based tours of data, in Javascript with R wrapper.

Assemblies from HPP Year 1 production

Ploidy agnostic phasing pipeline and algorithm

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

High-quality Nanopore-only genome polisher

Download FASTQ files from SRA or ENA repositories.

The Mojo Programming Language

Ultrafast Sample Placement on Existing Trees

A modern Python application packaging and distribution tool