minimap2

There are 26 repositories under minimap2 topic.

  • biowasm/biowasm

    WebAssembly modules for genomics

    Language:C195104218

  • jguhlin/minimap2-rs

    Rust bindings to minimap2 library

    Language:Rust5172010

  • CMU-SAFARI/SneakySnake

    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.org/abs/1910.09020.

    Language:VHDL469310
  • pafpy

    mbhall88/pafpy

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

    Language:Python31353

  • esteinig/vircov

    Viral genome coverage evaluation for metagenomic diagnostics :drop_of_blood:

    Language:Rust262174

  • mehdiborji/nanoranger

    simplified cellranger for long-read data

    Language:Python15143

  • kojix2/ruby-minimap2

    Powerful long read aligner for Ruby

    Language:Ruby14391

  • mbhall88/streamformatics

    Real-time species-typing visualisation for nanopore data.

    Language:JavaScript13624

  • CMU-SAFARI/Genome-on-Diet

    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).

    Language:Roff11714

  • abs-tudelft/variant-calling-at-scale

    Scalable and High Performance Variant Calling on Cluster Environments

    Language:Python10400

  • SanojPunchihewa/f5n

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

    Language:Java103607

  • CMU-SAFARI/Molecules2Variations

    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://arxiv.org/abs/2205.07957

    850

  • CMU-SAFARI/GateSeeder

    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.

    Language:C7600

  • akikuno/cstag

    Python module to manipulate and visualize minimap2's cs tag

    Language:Python61100

  • AntoineHo/SAVi

    Simple Alignment Viewer

    Language:Python6100

  • tpoorten/compareAssemblies

    Python script for comparing two genome assemblies

    Language:Python6211

  • alexomics/read-paf

    Scripts for reading minimap2 PAF files

    Language:Python4153

  • simpsonlab/preqclr

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

    Language:C++4402

  • AntoineHo/CircosAlignmentPlotter

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

    Language:Python3221

  • mjoppich/sequ-into

    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 applications. Furthermore, it might be unclear weather the sequenced reads represent the intended target. To address these issues we developed a cross-platform desktop application: Sequ-Into.

    Language:TypeScript3301

  • Licheng-Guo/minimap2-acceleration

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

    Language:C2000

  • lirepo/MLIA

    Mitochondrial Long-read Iterative Assembly

    Language:Python2201

  • fg6/forACT

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

    Language:C++0202

  • hiruna72/f5n

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

    Language:Java0100

  • mansikath/FASTQ-to-BAM

    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.

    0100

  • SanojPunchihewa/minimap2-arm

    A versatile pairwise aligner for genomic and spliced nucleotide sequences

    Language:C1