Glossary

This files contain a glossary of technical terms and concepts that are used in the documentation.

Alignement

File formats

An aligned file can be stored in different formats described below:

Format	Content	Compressed	Description	Specification
SAM	Textual	No	Base file format for aligned read	SAM format
BAM	Binary	No	Binary version of SAM	BAM format
CRAM	Binary	Yes	Highly compressed version of BAM	CRAM format
FASTA	Textual	No	For each sequence contains a single letter representing the nucleotide at a specific position.	It doesn't have a formal specification, more information here
GFF3	Textual	No	Annotation data	GFF3 format
VCF	Textual	No	Variant data
BCF	Binary	Yes (optional)	Variant data	BCF format

NOTE: The reality is more nuanced than what described in this table, as a SAM file can also contain unaligned reads, CRAM files can store uncompressed data, and there are many more details that are not described here for the sake of brevity. In any case, the table above contain the most common usages of these files, you can find more information by looking at their respective specifications.

TBD: add unaligned formats. FASTQ, Textual, DNA sequences with quality scores, Yes, FASTQ format