425 Open source projects that are alternatives of or similar to Awesome Cancer Variant Databases

Toolset for SV simulation, comparison and filtering

NGLess: NGS with less work

BioGrakn Knowledge Graph

A cool place to store your Hi-C

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Bio4j abstract model and general entry point to the project

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Reads simulator

Python module for average nucleotide identity analyses

R package for analyzing single-cell RNA-seq data

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

A powerful open source data warehouse system

SortMeRNA: next-generation sequence filtering and alignment tool

Package for fetching metadata and downloading data from SRA/ENA/GEO

microsatellite instability detection using tumor only or paired tumor-normal data

Rapid large-scale prokaryote pan genome analysis

A collection of scripts and notes related to genomics and bioinformatics

parallel fastq-dump wrapper

Inference of ploidy and heterozygosity structure using whole genome sequencing data

GenomeTools genome analysis system.

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

A DSL for data-driven computational pipelines

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Bioinformatics library for .NET

code for reading and processing Allen Institute for Brain Science data

A robust and fast clustering method for amplicon-based studies

Bayesian haplotype-based mutation calling

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

Annotated data.

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

A comprehensive library for computational molecular biology

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Protein Graph Library

Structural variant toolkit for VCFs

Fast multi-line FASTA/Q reader in several programming languages

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

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

EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.

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

Syntax highlighting for computational biology

ECG classification programs based on ML/DL methods

Flexible genotype query among 30,000+ samples whole-genome

Biological sequences for the julia language

Training and evaluating a variational autoencoder for pan-cancer gene expression data

An interactive web tool for quality control of DNA sequencing data

Tools for working with genomic and high throughput sequencing data.

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

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

The START App: R Shiny Transcriptome Analysis Resource Tool

Deep learning infrastructure for bioinformatics

Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

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

Single cell perturbation prediction

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results