SeqAn3
Search
Collaboration diagram for Search:

Modules

 Algorithm
 
 FM Index
 

Namespaces

 seqan3::search_cfg
 A special sub namespace for the search configurations.
 

Detailed Description

Introduction

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).

Todo:
Elaborate on that (space consumption for growing k, maybe a rule of thumb).

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.

Todo:
k-mer indices are coming soon. Stay tuned!