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Sneakysnake ⭐ 44

SneakySnake🐍 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.

ClairS - a deep-learning method for long-read somatic small variant calling

🍶Genome assembly with short sequence reads

Genomeanalysismodule ⭐ 21

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.

Fraggenescanrs ⭐ 10

Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.

A scalable variant calling and benchmarking framework supporting both short and long reads.

VStrains is a de novo approach for reconstructing strains from viral quasispecies.

Targeted Assembly of Short Reads

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