WebAssembly modules for genomics

Rust bindings to minimap2 library

SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.o…

A lightweight library for working with PAF (Pairwise mApping Format) files

Viral genome coverage evaluation for metagenomic diagnostics 🩸

Powerful long read aligner for Ruby

Real-time species-typing visualisation for nanopore data.

simplified cellranger for long-read data

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

Scalable and High Performance Variant Calling on Cluster Environments

Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https…

GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.

Simple Alignment Viewer

Python module to manipulate and visualize minimap2's cs tag

Python script for comparing two genome assemblies

Scripts for reading minimap2 PAF files

preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.

Third generation sequencing techniques rapidly evolved as a common practice in molecular biology. Great advances have been made in terms of feasibility, cost, throughput, and read-length. However, sample contamination still poses a big issue: it complicates correct, high-quality downstream analysis of sequencing data and usage in medical applica…

Converts a part of an alignment (.PAF perhaps others sometimes) to a Circos image using BED and fasta files.