Open source software
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https://github.com/zarr-developers/zarr-python - zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.
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https://github.com/cggh/scikit-allel - scikit-allel is a Python package for exploratory analysis of large scale genetic variation data.
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https://github.com/alimanfoo/pysamstats - pysamstats is a fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
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https://github.com/petl-developers/petl - petl is a general purpose Python package for extracting, transforming and loading tables of data.