WebAssembly modules for genomics
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Updated
Sep 26, 2024 - HTML
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…
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
Viral genome coverage evaluation for metagenomic diagnostics 🩸
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).
Real-time species-typing visualisation for nanopore data.
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.
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
Simple Alignment Viewer
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.
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