14 best Python Genomics libraries in 2025
by marketing.admin@openweaver.com 
Updated: Feb 2, 2023
Guide Kit
Python has become a primary language in the field of bioinformatics and computational biology. It is one of the best programming languages for scientific computing, data analysis, and analytics. It is also widely used by mathematicians and statisticians to create data-driven applications. The advent of next-generation sequencing technologies has enabled a revolution in genomic research. Python is also very popular in genomics and bioinformatics community due to the fact that it provides high level of abstraction, large number of available packages and great visualization tools. Genomics is a rapidly growing field with many new tools and techniques being developed every year. It can be used for various applications such as data analysis, statistical analysis, simulation and visualization. They have been tested on several different systems. A few of the most popular Python Genomics open source libraries for developers are: deepvariant - analysis pipeline that uses a deep neural network; hail - Scalable genomic data analysis; pyGenomeTracks - python module to plot beautiful.
deepvariantby google
2819 Version:v1.5.0DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
deepvariantby google
Python 2819 Version:v1.5.0 License: Permissive (BSD-3-Clause)
hailby hail-is
881 Version:0.2.117Cloud-native genomic dataframes and batch computing
hailby hail-is
Python 881 Version:0.2.117 License: Permissive (MIT)
pyGenomeTracksby deeptools
631 Version:3.8python module to plot beautiful and highly customizable genome browser tracks
pyGenomeTracksby deeptools
Python 631 Version:3.8 License: Strong Copyleft (GPL-3.0)
ncbi-genome-downloadby kblin
759 Version:0.3.1Scripts to download genomes from the NCBI FTP servers
ncbi-genome-downloadby kblin
Python 759 Version:0.3.1 License: Permissive (Apache-2.0)
jcviby tanghaibao
587 Version:CurrentPython library to facilitate genome assembly, annotation, and comparative genomics
jcviby tanghaibao
Python 587 Version:Current License: Permissive (BSD-2-Clause)
OrthoFinderby davidemms
549 Version:2.5.5Phylogenetic orthology inference for comparative genomics
OrthoFinderby davidemms
Python 549 Version:2.5.5 License: Strong Copyleft (GPL-3.0)
eggnog-mapperby eggnogdb
461 Version:2.1.11Fast genome-wide functional annotation through orthology assignment
eggnog-mapperby eggnogdb
Python 461 Version:2.1.11 License: Strong Copyleft (AGPL-3.0)
sourmashby sourmash-bio
368 Version:v4.8.2Quickly search, compare, and analyze genomic and metagenomic data sets.
sourmashby sourmash-bio
Python 368 Version:v4.8.2 License: Others (Non-SPDX)
pyGenoby tariqdaouda
286 Version:1.3.1Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
pyGenoby tariqdaouda
Python 286 Version:1.3.1 License: Permissive (Apache-2.0)
pyensemblby openvax
318 Version:v1.1.0Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
pyensemblby openvax
Python 318 Version:v1.1.0 License: Permissive (Apache-2.0)
sourmashby dib-lab
247 Version:v4.1.1Quickly search, compare, and analyze genomic and metagenomic data sets.
sourmashby dib-lab
Python 247 Version:v4.1.1 License: Others (Non-SPDX)
aws-batch-genomicsby aws-samples
178 Version:v2.0.0Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
aws-batch-genomicsby aws-samples
Python 178 Version:v2.0.0 License: Permissive (Apache-2.0)