WebAssembly modules for genomics

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…

Rust bindings to minimap2 library

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

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).

Viral genome coverage evaluation for metagenomic diagnostics 🩸

Real-time species-typing visualisation for nanopore data.

Scripts for reading minimap2 PAF files

simplified cellranger for long-read data

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

Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints

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

Powerful long read aligner for Ruby

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.

Python script for comparing two genome assemblies

Mitochondrial Long-read Iterative Assembly

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Scalable and High Performance Variant Calling on Cluster Environments

Simple Alignment Viewer