Jupyter Notebook sequencing

Open-source Jupyter Notebook projects categorized as sequencing
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Topics: Variants Genomics variant-calling hla-typing
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Jupyter Notebook sequencing Projects

  • HLA

    xHLA: Fast and accurate HLA typing from short read sequence data

    • Project mention: HLA-Genotyping | /r/Nebulagenomics | 2023-05-19

    xHLA on GitHub worked for me running it directly on the Nebula cram file with no additional processing. Results match those from OptiType (which had high memory requirements, was much slower and only covered 3 of the 6 common genes).

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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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).

Index

Project Stars
1 HLA 95

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