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

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

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

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

Assembling the cause of phenotypes and genotypes from NGS data

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

Antimicrobial Resistance Identification By Assembly

Rapid large-scale prokaryote pan genome analysis

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.

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

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

An interactive web tool for quality control of DNA sequencing data

Analysis pipelines for sequencing data

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

Intuitive local web frontend for the BLAST bioinformatics tool

Official code repository for GATK versions 4 and up

A package for designing compact and comprehensive capture probe sets.

Data intensive science for everyone.

Finds SNP sites from a multi-FASTA alignment file

Predict plasmids from uncorrected long read data

A collection of scripts and notes related to genomics and bioinformatics

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.

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

Inference of ploidy and heterozygosity structure using whole genome sequencing data

De novo assembly based variant calling pipeline for Illumina short reads

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

Earl Grey: A fully automated TE curation and annotation pipeline

annotate a VCF with other VCFs/BEDs/tabixed files

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Example client programs for Saphetor's VarSome annotation API

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

A cool place to store your Hi-C

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

A fast 23andMe genome text file parser, now superseded by arv

Efficient pythonic random access to fasta subsequences

A comprehensive tutorial about GWAS and PRS

GCP Essentials for Bioinformatics Researchers

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

An open source platform for managing and analyzing biomedical big data

Java utilities for Bioinformatics

A fast and sensitive gapped read aligner

The next version of bwa-mem

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

Bioinformatics library for .NET

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

A high-performance, Pythonic language for bioinformatics

A modern genome browser built with JavaScript and HTML5.

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

Tools to process and analyze deep sequencing data.

highly-efficient & lightweight mutation signature matrix aggregation

Scalable genomic data analysis.

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

UGENE is free open-source cross-platform bioinformatics software

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...)

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

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