Is there a tool that quantifies “spatial coverage”, that is what percentage of a reference assembly has a read mapped to it?

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  • mosdepth

    fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

    • I would give mosdepth a look. It can provide depth across a chromosome/contig at each base, or a mean depth for a given window size (eg 1kb), or regions provided within a bed file, or a simple summary of the mean depth across each chromosome/contig.

  • 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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