Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

Nanopore sequence read simulator

Sequence correction provided by ONT Research

Clustering and Serotyping of Shigatoxin producing E. coli (STEC) using genomic cluster specific markers

Script for in silico serotyping of e. Coli.

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Signal-level algorithms for MinION data

adapter trimmer for Oxford Nanopore reads

Trimming tool for Oxford Nanopore sequence data

Tips for Nextflow and cheatsheet for channel operation

Implementation of Krona to QIIME2

Classifier for metagenomic sequences using FM-index with run-block compressed BWT.

A simple pipeline for bacterial assembly and quality control

Estimate the relative abundance of sequence reads originating from different species in a sample.

Pathoscope: Species identification and strain attribution with unassembled sequencing data

Long-read metagenomic analysis

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

quality filtering tool for long reads

Toxoid sequences of all known Shiga Toxin subtypes (1a, 1c-e; 2a-o) in fasta format

Detection of incorrectly labeled sequences across kingdoms

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

Oxford Nanopore's Basecaller

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Genome assembly evaluation tool

🆔 Scan contig files against PubMLST typing schemes

Long read aligner

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Classifier for metagenomic sequences