934 Open source projects that are alternatives of or similar to Gubbins

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

A tool to circularize genome assemblies

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

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

Assembling the cause of phenotypes and genotypes from NGS data

Antimicrobial Resistance Identification By Assembly

Rapid large-scale prokaryote pan genome analysis

Finds SNP sites from a multi-FASTA alignment file

Multilocus sequence typing by blast using the schemes from PubMLST

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

Predict plasmids from uncorrected long read data

Data intensive science for everyone.

An interactive web tool for quality control of DNA sequencing data

Intuitive local web frontend for the BLAST bioinformatics tool

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

Genomics Extension for SQLite

A collection of scripts and notes related to genomics and bioinformatics

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

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

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

Analysis pipelines for sequencing data

Fast hash function for DNA sequences

Compute N50/NG50 and auN/auNG

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Provide R access to the NCI Genomic Data Commons portal.

Bystro genetic analysis (annotation, filtering, statistics)

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Fast alignment and preprocessing of chromatin profiles

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Simple pure Python SAM parser and objects for working with SAM records

An open-access bioinformatics text

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

A fast 23andMe genome text file parser, now superseded by arv

A curated list of awesome bioinformatics software.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Earl Grey: A fully automated TE curation and annotation pipeline

BACNET is a Java based platform to develop website for multi-omics analysis

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.

Example client programs for Saphetor's VarSome annotation API

annotate a VCF with other VCFs/BEDs/tabixed files

dysgu-SV is a collection of tools for calling structural variants using short or long reads

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

De novo assembly based variant calling pipeline for Illumina short reads

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A React web application to query and share any PostgreSQL database.

Efficient pythonic random access to fasta subsequences

A comprehensive tutorial about GWAS and PRS

Java utilities for Bioinformatics

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

An open source platform for managing and analyzing biomedical big data

Model and predict short DNA sequence features with neural networks

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

A modern genome browser built with JavaScript and HTML5.

A fast and sensitive gapped read aligner

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

The next version of bwa-mem

A high-performance, Pythonic language for bioinformatics