1D/2D indexing and querying with a pair of genomic coordinates
DescriptionPairix is a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates. Pairix is a stand-alone C program that was written on top of tabix as a tool for the 4DN-standard pairs file format describing Hi-C data: pairs_format_specification.md However, Pairix can be used as a generic tool for indexing and querying any bgzipped text file containing genomic coordinates, for either 2D- or 1D- indexing and querying. For example: given the custom text file below, you want to extract specific lines from the Pairs file further below. An awk command would read the Pairs file from beginning to end. Pairix creates an index and uses it to access the file from a relevant position by taking advantage of bgzf compression, allowing for a fast query on large files.
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Install this software package
If the package is available for the distribution you are currently using on your computer then install the software by clicking on…Install python3-pairix