Scalable and High Performance Variant Calling on Cluster Environments

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.

[FCCM 2019] Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: A Race Between FPGA and GPU

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…

Python module to manipulate and visualize minimap2's cs tag

Genopo a.k.a. F5N - a portable DNA analysis toolkit for nanopore data https://nanoporetech.com

This repository streamlines the conversion of raw DNA sequencing data from FASTQ to BAM format, incorporating scripts that not only facilitate BAM conversion but also generate Sequence Alignment Map (SAM) files.

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

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.

Scripts for reading minimap2 PAF files

simplified cellranger for long-read data

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

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).