1007 Open source projects that are alternatives of or similar to Abyss

🌈Scaffold genome sequence assemblies using linked read sequencing data

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A package for designing compact and comprehensive capture probe sets.

Official code repository for GATK versions 4 and up

Classify sequencing reads using MinHash.

GenomeTools genome analysis system.

www.eemodelingsystem.com

library of C++ functions that support applications of Stan in Pharmacometrics

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

This is a set of simple programs that can be used to explore the features of a parallel platform.

Java utilities for Bioinformatics

Parallel Matrix Multiplication Using OpenMP, Phtreads, and MPI

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Análisis numérico y cómputo científico

This repository consists for gpu bootcamp material for HPC and AI

Highly parallel DBSCAN (HPDBSCAN)

An analysis and visualization platform for 'omics data

wxParaver is a trace-based visualization and analysis tool designed to study quantitative detailed metrics and obtain qualitative knowledge of the performance of applications, libraries, processors and whole architectures.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software. Modularity, extensibility and HPC are the main objectives. Kratos has BSD license and is written in C++ with extensive Python interface.

RAxML Next Generation: faster, easier-to-use and more flexible

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Data and analysis for the Splatter paper

Curated (meta)list of resources for Biology.

🚀 Fast prime counting function implementations

Dynamic execution environments for coupled, thread-heterogeneous MPI+X applications

This repository collects the materials from the course "Foundations of HPC", 2021, at the Data Science and Scientific Computing Department, University of Trieste

UCL-RITS *C++ for Research* engineering course

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

A genome browser that shows long reads and complex variants better

YASK--Yet Another Stencil Kit: a domain-specific language and framework to create high-performance stencil code for implementing finite-difference methods and similar applications.

Fast hash function for DNA sequences

Ytk-mp4j is a fast, user-friendly, cross-platform, multi-process, multi-thread collective message passing java library which includes gather, scatter, allgather, reduce-scatter, broadcast, reduce, allreduce communications for distributed machine learning.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

UGENE is free open-source cross-platform bioinformatics software

NGLess: NGS with less work

Python extension language using accelerators

A parallel, fast solver for the scalar advection-diffusion and the incompressible Navier-Stokes equations based on semi-Lagrangian/Volume-Integral method.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

This library tackles the construction and efficient execution of computational chemistry workflows

A repository for setting up a RNAseq workflow

John the Ripper jumbo - advanced offline password cracker, which supports hundreds of hash and cipher types, and runs on many operating systems, CPUs, GPUs, and even some FPGAs

High-performance stateful serverless runtime based on WebAssembly

Data intensive science for everyone.

C++ library for solving large sparse linear systems with algebraic multigrid method

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Extreme-scale Discontinuous Galerkin Environment (EDGE)

Signal-level algorithms for MinION data

Next generation sequencing reads de novo assembler.

A collection of scripts and notes related to genomics and bioinformatics

A collection of code examples as well as presentations for training purposes

Plant image analysis using OpenCV

Open source repository for QuickPIC

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Kubernetes Operator for Allreduce-style Distributed Training

code for reading and processing Allen Institute for Brain Science data

The HPC toolbox: fused matrix multiplication, convolution, data-parallel strided tensor primitives, OpenMP facilities, SIMD, JIT Assembler, CPU detection, state-of-the-art vectorized BLAS for floats and integers

A curated list of resources for learning bioinformatics.