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API Reference
Here is a list of all topics with brief descriptions:

Sequence Alignment | The alignment module contains concepts, algorithms and classes that are related to the computation of pairwise and multiple sequence alignments
Aligned Sequence | Provides seqan3::aligned_sequence, as well as various ranges that model it
CIGAR Conversion | The CIGAR Conversion submodule contains utility functions to convert a CIGAR to an alignment or vice versa
Configuration | Provides configuration elements for the pairwise alignment configuration
Decorator | The decorator submodule contains special SeqAn decorators
Matrix | Provides data structures for representing alignment coordinates and alignments as a matrix
Pairwise Alignments | Provides the algorithmic components for the computation of pairwise alignments
Scoring | Provides the data structures used for scoring alphabets and sequences
Alphabet |
Adaptation | Provides alphabet adaptions of some standard char and uint types
Aminoacid | Provides the amino acid alphabets and functionality for translation from nucleotide
CIGAR | Provides (semi-)alphabets for representing elements in CIGAR strings
Composite | Provides templates for combining existing alphabets into new alphabet types
Container | Alphabet related container
Gap | Provides the gap alphabet and functionality to make an alphabet a gapped alphabet
Mask | Provides the mask alphabet and functionality for creating masked composites
Nucleotide | Provides the different DNA and RNA alphabet types
Range | Alphabet related ranges
Structure | Provides types to represent single elements of RNA and protein structures
Views | Alphabet related views
Argument Parser |
Core | Provides core functionality used by multiple modules
Algorithm | Provides core functionality used for algorithms
Concept | Provides core concepts
Configuration | Provides core functionality used to configure configurations
Debug Stream | Provides core functionality used to print seqan3 and std types
Range | Provides seqan3 general purpose range functionality
IO | The IO module provides stream handling formatted I/O
SAM File | Provides files and formats for handling read mapping data
Sequence File | Provides files and formats for handling sequence data
Stream | The stream sub-module contains data structures and functions for streaming and tokenization
Structure File | Provides files and formats for handling structure data
Views | IO related views
Search | Data structures and approximate string search algorithms for large collection of text (e.g. DNA)
Configuration | Data structures and utility functions for configuring search algorithm
DREAM Index | Provides seqan3::interleaved_bloom_filter
FM Index | Provides seqan3::fm_index and seqan3::bi_fm_index as well as respective cursors
k-mer Index | Implementation of shapes for a k-mer Index
Views | Search related views
std | A subset of the C++20 standard library made available in pre-C++20 contexts
charconv | The <charconv> header from C++17's standard library
new | The <new> header from C++17's standard library
Utility | Provides additional utility functionality used by multiple modules
Bloom Filter | Provides seqan3:bloom_filter
Builtin Character Operations | Provides various operations on character types
Concept | Provides various general purpose concepts
Container | Provides various general purpose container and concepts
Range | The range module provides general purpose range concepts
Tuple | Additional helper utilities for "tuple" types like std::tuple, std::pair, seqan3::pod_tuple that are not specific to a SeqAn module
Type List | Provides seqan3::type_list and metaprogramming utilities for working on type lists
Type Pack | Provides metaprogramming utilities for working on template parameter packs
Type Traits | Provides various type traits and their shortcuts
Views | Views are "lazy range combinators" that offer modified views onto other ranges

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