Modules | |
Algorithm | |
FM Index | |
Namespaces | |
seqan3::search_cfg | |
A special sub namespace for the search configurations. | |
Searching is a key component in many sequence analysis tools. The search module is a powerful and easy way to search sequences in a large text or an arbitrary nested collection of texts. When it comes to searching, indices are a core component for searching large amounts of data and are used for tools such as read mappers, assemblers or protein search tools. There are currently two major kind of indices: FM indices and k-mer indices (also known as q-gram indices).
Generally speaking k-mer indices support very fast searching of exact k-mers (strings of length k) or k-mers with predefined wildcard positions that do not have to match. FM indices on the other hand are more versatile and work with arbitrary pattern lengths and error numbers / positions.
SeqAn3 currently supports very fast FM indices. For more details visit the FM Index submodule.