Bam viewer with custom fasta reference that's embeddable in Streamlit app?

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  • pybamview

    Browser based application for viewing bam alignments

  • pybamview is very old, requires python 2.6 and doesen't provide and API, so it requires CLI calls to be performed from my scripts.

  • igv-notebook

    Module for embedding igv.js in an IPython notebook

  • igv-notebook and igv-jupyter seem amazing but (unsurprisingly) I could not get them to run anywhere that wasn't a jupyter notebook. I get a kernel error as it tries to initialize itself within streamlit, and I'm not sure how to embed it anywhere else.

  • 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.

    InfluxDB logo
  • igv-jupyter

    Extension for Jupyter which integrates igv.js

  • igv-notebook and igv-jupyter seem amazing but (unsurprisingly) I could not get them to run anywhere that wasn't a jupyter notebook. I get a kernel error as it tries to initialize itself within streamlit, and I'm not sure how to embed it anywhere else.

  • ipyigv

    A Jupyter wrapper for the igv.js library (representation of genomic data)

  • ipyigv is the lower level version of these. I found no documentation on how it's supposed to be used, but I'll try to get it to work as a last option, maybe raising a new webserver\docker container and supplying the files to it.

  • dash-bio

    Open-source bioinformatics components for Dash

  • dash-bio This is another great choice, but unlike standard plotly figures, I need to find how to embedd dash widgets into streamlit. It seems possible, but it's not clear how to do it.

  • tinycov

    Command line tool to plot genomic coverage from a BAM file

  • tinycov I keep finding these small tools built with python, but with no API available, so they require a combination of CLI and Docker to work

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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