680 Open source projects that are alternatives of or similar to snp-sites

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Improve the quality of a denovo assembly by scaffolding and gap filling

Multilocus sequence typing by blast using the schemes from PubMLST

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Assembling the cause of phenotypes and genotypes from NGS data

Predict plasmids from uncorrected long read data

Antimicrobial Resistance Identification By Assembly

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Rapid large-scale prokaryote pan genome analysis

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

A tool to circularize genome assemblies

Command line utility for manipulating Illumina-generated FastQ files.

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

A collection of publications on comparison of high-throughput sequencing technologies.

Data intensive science for everyone.

An interactive web tool for quality control of DNA sequencing data

Bystro genetic analysis (annotation, filtering, statistics)

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Tools for analyzing 10X Genomics data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Collection of scripts for bacterial genomics

xHLA: Fast and accurate HLA typing from short read sequence data

Analysis pipelines for sequencing data

Genomics Extension for SQLite

A collection of scripts and notes related to genomics and bioinformatics

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

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

A modular annotation tool for genomic variants

Official code repository for GATK versions 4 and up

A package for designing compact and comprehensive capture probe sets.

Intuitive local web frontend for the BLAST bioinformatics tool

A Java API for high-throughput sequencing data (HTS) formats.

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Rare variant test software for next generation sequencing data

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

Distributed git repository manager

Phage-Host Interaction Search Tool

Python package and CLI for whole-genome duplication related analyses

PatZilla is a modular patent information research platform and data integration toolkit with a modern user interface and access to multiple data sources.

Here we collect and discuss the best DeFI & Blockchain researches and tools. Feel free to DM me on Twitter or open pool request.

Population assignment analysis using R

Learn the Deep Learning for Computer Vision in three steps: theory from base to SotA, code in PyTorch, and space-repetition with Anki

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

simuG: a general-purpose genome simulator

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Useful links of different content related to AI, Computer Vision, and Robotics.

Different mesh shading techniques using the NVIDIA RTX (Turing) technology.

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Seven Bridges Genomics aligner/caller debugging and analysis tools

High-performance error correction for Illumina resequencing data

An index of algorithms for offline reinforcement learning (offline-rl)

Crawl all your citations from Google Scholar

Alpha from various sectors in the blockchain space.

A (WIP) TensorFlow reproduction of Fu, Huang, Ding, Liao, and Paisley's method for single-image rain removal (https://arxiv.org/abs/1609.02087)

Nightcore: Efficient and Scalable Serverless Computing for Latency-Sensitive, Interactive Microservices [ASPLOS '21]