WebAssembly modules for genomics

• UpdatedFeb 12, 2025
• HTML

Rust bindings to minimap2 library

• UpdatedJan 9, 2025
• Jupyter Notebook

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…

• UpdatedMar 31, 2023
• VHDL

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

• UpdatedMay 3, 2022
• Python

Viral genome coverage evaluation for metagenomic diagnostics 🩸

• UpdatedDec 10, 2024
• Rust

simplified cellranger for long-read data

• UpdatedSep 18, 2024
• Python

Powerful long read aligner for Ruby

• UpdatedJan 17, 2025
• Ruby

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).

• UpdatedSep 4, 2024
• Roff

Real-time species-typing visualisation for nanopore data.

• UpdatedApr 11, 2023
• JavaScript

Nextflow Alignment Pipeline - DNAseq RNAseq

• UpdatedMar 15, 2025
• Nextflow

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

• UpdatedAug 2, 2021
• Java

Python module to manipulate and visualize minimap2's cs tag

• UpdatedJul 28, 2024
• Python

Scalable and High Performance Variant Calling on Cluster Environments

• UpdatedFeb 13, 2022
• Python

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.

• UpdatedOct 3, 2023
• C

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…

• UpdatedJun 14, 2022

Python script for comparing two genome assemblies

• UpdatedJan 22, 2018
• Python

Simple Alignment Viewer

• UpdatedSep 29, 2021
• Python

Scripts for reading minimap2 PAF files

• UpdatedFeb 23, 2023
• Python

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

• UpdatedSep 10, 2018
• C++

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…

• UpdatedMay 9, 2020
• TypeScript