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Top 23 Python Bioinformatic Projects
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I also like contributing specifically to my field. As a PhD student and possibly future scientist, I have a vested interest in the quality of the software in my field–specifically, structural bioinformatics. I use several tools in this field and often find areas that can be improved, both for myself and others. As an example, consider this minor documentation change I added to the Biopython documentation.
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deepvariant
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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deep_gcns_torch
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
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InfluxDB
InfluxDB – Built for High-Performance Time Series Workloads. InfluxDB 3 OSS is now GA. Transform, enrich, and act on time series data directly in the database. Automate critical tasks and eliminate the need to move data externally. Download now.
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scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
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GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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NOTE:
The open source projects on this list are ordered by number of github stars.
The number of mentions indicates repo mentiontions in the last 12 Months or
since we started tracking (Dec 2020).
Python Bioinformatics discussion
Python Bioinformatics related posts
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Workflow Engine for In-Silico Biology
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Circular Data Visualization in Python
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R pipelines for bulk RNA-seq analyses
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Nextflow: Data-Driven Computational Pipelines
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Invitación a proyecto - Biopython en Español
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Bam viewer with custom fasta reference that's embeddable in Streamlit app?
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Forums/Communites for Bioinformatics on Other Platforms?
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A note from our sponsor - SaaSHub
www.saashub.com | 1 Sep 2025
Index
What are some of the best open-source Bioinformatic projects in Python? This list will help you:
| # | Project | Stars |
|---|---|---|
| 1 | dash | 23,995 |
| 2 | Biopython | 4,710 |
| 3 | deepvariant | 3,482 |
| 4 | scanpy | 2,173 |
| 5 | scispacy | 1,862 |
| 6 | galaxy | 1,589 |
| 7 | deep_gcns_torch | 1,170 |
| 8 | ncbi-genome-download | 1,026 |
| 9 | Hail | 1,026 |
| 10 | scikit-bio | 964 |
| 11 | pyCirclize | 946 |
| 12 | biotite | 851 |
| 13 | PyDESeq2 | 671 |
| 14 | DnaFeaturesViewer | 649 |
| 15 | dash-cytoscape | 652 |
| 16 | Sniffles | 613 |
| 17 | clinker | 606 |
| 18 | biostar-central | 586 |
| 19 | redun | 556 |
| 20 | dash-bio | 557 |
| 21 | bakta | 544 |
| 22 | GTDBTk | 541 |
| 23 | sourmash | 519 |
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