398 Open source projects that are alternatives of or similar to Bioinf Python

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

dna2vec: Consistent vector representations of variable-length k-mers

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

Simple simulation of single-cell RNA sequencing data

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Next generation sequencing reads de novo assembler.

Single cell perturbation prediction

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

An efficient FASTQ manipulation suite

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

nim wrapper for htslib for parsing genomics data files

A Practical and Efficient NCBI Taxonomy Toolkit

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Annotated data.

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

R package for analyzing single-cell RNA-seq data

Application for making ENCODE Blacklists

Rapid large-scale prokaryote pan genome analysis

APBS - software for biomolecular electrostatics and solvation

parallel fastq-dump wrapper

UGENE is free open-source cross-platform bioinformatics software

Syntax highlighting for computational biology

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

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

A comprehensive library for computational molecular biology

SortMeRNA: next-generation sequence filtering and alignment tool

Bioconductor cheat sheet

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

Curated (meta)list of resources for Biology.

BioGrakn Knowledge Graph

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Genome assembly evaluation tool

ECG classification programs based on ML/DL methods

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.

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

A repository for setting up a RNAseq workflow

A tool to circularize genome assemblies

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

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

Ten Quick Tips for Deep Learning in Biology

NGLess: NGS with less work

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

A cool place to store your Hi-C

Tools for working with genomic and high throughput sequencing data.

Bio4j abstract model and general entry point to the project

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

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

Cuneiform distributed programming language

Python module for average nucleotide identity analyses

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

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

Bayesian haplotype-based mutation calling

Toolset for SV simulation, comparison and filtering

Reads simulator

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

The sources of the openSNP website

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page: