Glossary
===========



.. glossary::
    :sorted:

    Module
        A directory that contains a snakemake rule and an associated README file. 
        This is especially relevant for the Sequana pipelines. See :ref:`developers`.

    Snakefile
        A file that contains one or several Snakemake rules

    SAM
        Sequence Alignment Map is a generic nucleotide alignment format that
        describes the alignment of query sequences or sequencing reads to a reference
        sequence or assembly

    BAM

        Binary version of the Sequence Alignment Map (SAM) format.

    BAI

        The index file for a file generated in the BAM format. (This is a
        non-standard file type.)

    DSRC

        A compression tool dedicated to FastQ files

    FASTA

        FASTA-formatted sequence files contains either nucleic acid sequence
        (such as DNA) or protein sequence information. FASTA files store multiple
        sequences in a single file. 

    GFF

        General Feature Format, used for describing genes and other features
        associated with DNA, RNA and Protein sequences. 

    VCF

        Variant Call Format, for use with the variant calling pipeline

    BED

        Format that defines the data lines displayed in an annotation track.

    JSON

        A human-readable data serialization language commonly used in
        configuration files. See https://en.wikipedia.org/wiki/JSON

    YAML

        A human-readable data serialization language commonly used in
        configuration files. See https://en.wikipedia.org/wiki/YAML