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

tools for working with genome variation graphs

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

🔬 BEDOPS: high-performance genomic feature operations

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

A simple command-line tool to download data from Joint Genome Institute databases

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Fast hash function for DNA sequences

A modern genome browser built with JavaScript and HTML5.

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

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

A powerful open source data warehouse system

Deep learning infrastructure for bioinformatics

Compute N50/NG50 and auN/auNG

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

Modelling the Language of Life - Deep Learning Protein Sequences

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

Assembling the cause of phenotypes and genotypes from NGS data

Ten Quick Tips for Deep Learning in Biology

Provide R access to the NCI Genomic Data Commons portal.

Reads simulator

An open-access bioinformatics text

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

De novo assembly based variant calling pipeline for Illumina short reads

A tool to circularize genome assemblies

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

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

cython + htslib == fast VCF and BCF processing

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

annotate a VCF with other VCFs/BEDs/tabixed files

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

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A cool place to store your Hi-C

🧬 An R package for visualizing molecular data in 3D

A comprehensive tutorial about GWAS and PRS

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

Example client programs for Saphetor's VarSome annotation API

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

The next version of bwa-mem

Scripts to download genomes from the NCBI FTP servers

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

Scalable genomic data analysis.

Antimicrobial Resistance Identification By Assembly

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

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

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

An interactive web tool for quality control of DNA sequencing data

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

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

Model and predict short DNA sequence features with neural networks

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

Bayesian genotyper for structural variants

Genomics Extension for SQLite

GCP Essentials for Bioinformatics Researchers

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

A fast whole-genome aligner based on de Bruijn graphs