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

A tool to circularize genome assemblies

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

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

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

Finds SNP sites from a multi-FASTA alignment file

A collection of scripts and notes related to genomics and bioinformatics

Data intensive science for everyone.

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

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

Genomics Extension for SQLite

Analysis pipelines for sequencing data

Official code repository for GATK versions 4 and up

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.

An interactive web tool for quality control of DNA sequencing data

Multilocus sequence typing by blast using the schemes from PubMLST

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

Intuitive local web frontend for the BLAST bioinformatics tool

A package for designing compact and comprehensive capture probe sets.

Predict plasmids from uncorrected long read data

A fast and sensitive gapped read aligner

A modern genome browser built with JavaScript and HTML5.

The next version of bwa-mem

Ultra-fast and memory-efficient (meta-)genome assembler

Java utilities for Bioinformatics

Python library to facilitate genome assembly, annotation, and comparative genomics

Efficient pythonic random access to fasta subsequences

Tools to process and analyze deep sequencing data.

Scripts to download genomes from the NCBI FTP servers

Python and C++ code for reading and writing genomics data.

A comprehensive tutorial about GWAS and PRS

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Scalable genomic data analysis.

A repository for setting up a RNAseq workflow

Efficient variant-call data storage and retrieval library using the TileDB storage library.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

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

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

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

An open source platform for managing and analyzing biomedical big data

highly-efficient & lightweight mutation signature matrix aggregation

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

Model and predict short DNA sequence features with neural networks

A curated list of bioinformatics bench-marking papers and resources.

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Bayesian genotyper for structural variants

Structural variant toolkit for VCFs

A fast whole-genome aligner based on de Bruijn graphs

Bioinformatics library for .NET

Inference of ploidy and heterozygosity structure using whole genome sequencing data

GCP Essentials for Bioinformatics Researchers

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

UGENE is free open-source cross-platform bioinformatics software

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads