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14 best Python Genomics libraries in 2022

by Open Weaver kits ✔ Updated: May 13, 2022

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

Python star image 2686 Version:v1.4.0

License: Permissive (BSD-3-Clause)

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

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deepvariantby google

Python star image 2686 Version:v1.4.0 License: Permissive (BSD-3-Clause)

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

Python star image 854 Version:0.2.107

License: Permissive (MIT)

Scalable genomic data analysis.

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hailby hail-is

Python star image 854 Version:0.2.107 License: Permissive (MIT)

Scalable genomic data analysis.
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pyGenomeTracksby deeptools

Python star image 539 Version:3.6

License: Strong Copyleft (GPL-3.0)

python module to plot beautiful and highly customizable genome browser tracks

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pyGenomeTracksby deeptools

Python star image 539 Version:3.6 License: Strong Copyleft (GPL-3.0)

python module to plot beautiful and highly customizable genome browser tracks
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ncbi-genome-downloadby kblin

Python star image 706 Version:0.3.1

License: Permissive (Apache-2.0)

Scripts to download genomes from the NCBI FTP servers

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ncbi-genome-downloadby kblin

Python star image 706 Version:0.3.1 License: Permissive (Apache-2.0)

Scripts to download genomes from the NCBI FTP servers
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jcviby tanghaibao

Python star image 499 Version:1.2.20

License: Permissive (BSD-2-Clause)

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

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jcviby tanghaibao

Python star image 499 Version:1.2.20 License: Permissive (BSD-2-Clause)

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

Python star image 499 Version:2.5.4

License: Strong Copyleft (GPL-3.0)

Phylogenetic orthology inference for comparative genomics

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OrthoFinderby davidemms

Python star image 499 Version:2.5.4 License: Strong Copyleft (GPL-3.0)

Phylogenetic orthology inference for comparative genomics
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eggnog-mapperby eggnogdb

Python star image 414 Version:2.1.9

License: Strong Copyleft (AGPL-3.0)

Fast genome-wide functional annotation through orthology assignment

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eggnog-mapperby eggnogdb

Python star image 414 Version:2.1.9 License: Strong Copyleft (AGPL-3.0)

Fast genome-wide functional annotation through orthology assignment
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sourmashby sourmash-bio

Python star image 344 Version:4.6.1

License: Others (Non-SPDX)

Quickly search, compare, and analyze genomic and metagenomic data sets.

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sourmashby sourmash-bio

Python star image 344 Version:4.6.1 License: Others (Non-SPDX)

Quickly search, compare, and analyze genomic and metagenomic data sets.
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pyrangesby biocore-ntnu

Python star image 331 Version:0.0.111

License: Permissive (MIT)

Performant Pythonic GenomicRanges

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pyrangesby biocore-ntnu

Python star image 331 Version:0.0.111 License: Permissive (MIT)

Performant Pythonic GenomicRanges
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pyGenoby tariqdaouda

Python star image 286 Version:1.3.1

License: Permissive (Apache-2.0)

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

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pyGenoby tariqdaouda

Python star image 286 Version:1.3.1 License: Permissive (Apache-2.0)

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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pyensemblby openvax

Python star image 318 Version:2.2.4

License: Permissive (Apache-2.0)

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

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pyensemblby openvax

Python star image 318 Version:2.2.4 License: Permissive (Apache-2.0)

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
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sourmashby dib-lab

Python star image 247 Version:0.11.0

License: Others (Non-SPDX)

Quickly search, compare, and analyze genomic and metagenomic data sets.

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sourmashby dib-lab

Python star image 247 Version:0.11.0 License: Others (Non-SPDX)

Quickly search, compare, and analyze genomic and metagenomic data sets.
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genomepyby vanheeringen-lab

Python star image 282 Version:0.14.0

License: Permissive (MIT)

genes and genomes at your fingertips

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genomepyby vanheeringen-lab

Python star image 282 Version:0.14.0 License: Permissive (MIT)

genes and genomes at your fingertips
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aws-batch-genomicsby aws-samples

Python star image 178 Version:v2.0.0

License: Permissive (Apache-2.0)

Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.

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aws-batch-genomicsby aws-samples

Python star image 178 Version:v2.0.0 License: Permissive (Apache-2.0)

Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
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