676 Open source projects that are alternatives of or similar to Biopython

Analysis pipelines for sequencing data

Data intensive science for everyone.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

A collection of scripts and notes related to genomics and bioinformatics

Fast and flexible ORF finder

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

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

A curated list of awesome bioinformatics software.

Official code repository for GATK versions 4 and up

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

A package for designing compact and comprehensive capture probe sets.

Neural Networks for Protein Sequence Alignment

A fast 23andMe genome text file parser, now superseded by arv

Efficient pythonic random access to fasta subsequences

tools for working with genome variation graphs

🔬 BEDOPS: high-performance genomic feature operations

A genome browser that shows long reads and complex variants better

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Deep learning infrastructure for bioinformatics

Ten Quick Tips for Deep Learning in Biology

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

An interactive web tool for quality control of DNA sequencing data

Scalable genomic data analysis.

cython + htslib == fast VCF and BCF processing

GenomeTools genome analysis system.

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

A fast whole-genome aligner based on de Bruijn graphs

An ultrafast memory-efficient short read aligner

Proof-of-concept seq-to-graph mapper and graph generator

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

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

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

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

Model and predict short DNA sequence features with neural networks

Reads simulator

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

Rapid large-scale prokaryote pan genome analysis

Bayesian genotyper for structural variants

Scripts to download genomes from the NCBI FTP servers

Antimicrobial Resistance Identification By Assembly

GCP Essentials for Bioinformatics Researchers

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Bioinformatics library for .NET

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.

NGLess: NGS with less work

Intuitive local web frontend for the BLAST bioinformatics tool

A Java API for high-throughput sequencing data (HTS) formats.

Genomics Extension for SQLite

A cool place to store your Hi-C

A tool to circularize genome assemblies

A powerful open source data warehouse system

nim wrapper for htslib for parsing genomics data files

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

Bayesian haplotype-based mutation calling