tools for working with genome variation graphs

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

A single molecule sequence assembler for genomes large and small.

hybrid assembly pipeline for bacterial genomes

Oxford Nanopore's Basecaller

Mummer alignment tool

Fast genome and metagenome distance estimation using MinHash

adapter trimmer for Oxford Nanopore reads

quality filtering tool for long reads

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Classifier for metagenomic sequences

De novo genome assembler for long uncorrected reads

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output inc…

Ultrafast Sample Placement on Existing Trees

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Efficient phylogenetic tree inference for massive taxonomic datasets

A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Bifrost graph gene caller.

Ultra-fast preprocessing and quality control for long-read sequencing data

✏️ Genome assembly polishing & SNV detection

Mumemto: multi-MUM and MEM finding across pangenomes

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

Fast and space-efficient taxonomic classification of long reads

kmerfreq count K-mer (with size K) frequency from the input sequence data, typically sequencing reads data, and refe rence genome data is also applicable. Kmerferq output file can be used as input …

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

Framework of alignment-free method for variants detection.

STX operon typing

A fast tool for constructing distance matrices from bacterial genomes