Java utilities for Bioinformatics

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

A curated list of resources for learning bioinformatics.

Rapid large-scale prokaryote pan genome analysis

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

An efficient FASTQ manipulation suite

Finds SNP sites from a multi-FASTA alignment file

A tool to circularize genome assemblies

Antimicrobial Resistance Identification By Assembly

Rare variant test software for next generation sequencing data

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Get assembly statistics from FASTA and FASTQ files

Infectious Disease Sequencing Platform

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Improve the quality of a denovo assembly by scaffolding and gap filling

de novo virus assembler of Illumina paired reads

Python3 scripts to manipulate FASTA and FASTQ files

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

DeepMicrobes: taxonomic classification for metagenomics with deep learning

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

My own tools code for NGS data analysis (Next Generation Sequencing)

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)