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

De novo assembly based variant calling pipeline for Illumina short reads

UGENE is free open-source cross-platform bioinformatics software

A repository for setting up a RNAseq workflow

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

Bayesian genotyper for structural variants

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Deep learning infrastructure for bioinformatics

Ten Quick Tips for Deep Learning in Biology

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

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

Model and predict short DNA sequence features with neural networks

Code examples of fast and simple k-mer counters for tutorial purposes

Java utilities for Bioinformatics

JavaScript VisualizationTools

Official git repository for Biopython (originally converted from CVS)

GCP Essentials for Bioinformatics Researchers

cython + htslib == fast VCF and BCF processing

A fast and sensitive gapped read aligner

An open source platform for managing and analyzing biomedical big data

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

NGLess: NGS with less work

An ultrafast memory-efficient short read aligner

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Toolkit for preparing genomes for submission to NCBI

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

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Scripts to download genomes from the NCBI FTP servers

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

Scalable genomic data analysis.

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

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

Provide R access to the NCI Genomic Data Commons portal.

highly-efficient & lightweight mutation signature matrix aggregation

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Earl Grey: A fully automated TE curation and annotation pipeline

A fast 23andMe genome text file parser, now superseded by arv

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.

An open-access bioinformatics text

annotate a VCF with other VCFs/BEDs/tabixed files

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A high-performance, Pythonic language for bioinformatics

Example client programs for Saphetor's VarSome annotation API

Efficient pythonic random access to fasta subsequences

A comprehensive tutorial about GWAS and PRS

Bystro genetic analysis (annotation, filtering, statistics)

Tools to process and analyze deep sequencing data.

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

The next version of bwa-mem

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

Structural variant toolkit for VCFs

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

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

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

A modern genome browser built with JavaScript and HTML5.

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

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

pymzML - an interface between Python and mzML Mass spectrometry Files

UXF - Framework for creating human behaviour experiments in Unity