Crate debruijn

debruijn: a De Bruijn graph library for DNA seqeunces in Rust.

This library provides tools for efficient construction DeBruijn graphs (dBG) from DNA sequences, tracking arbitrary metadata associated with kmers in the graph, and performing path-compression of unbranched graph paths to improve speed and reduce memory consumption.

Most applications of debruijn will follow this general workflow:

1. You generate a set of sequences to make a dBG from.
2. You pass those sequences to the filter_kmers function, which converts the sequences into kmers, while tracking 'metadata' about each kmer in a very customizable way. The metadata could be read count, a set of colors, a set of read counts split by haplotype, a UMI count, etc.
3. The the library will convert the kmers to a compressed dBG. You can also customize the rules for how to compress the dBG and how to 'combine' the per-kmer metadata.

Then you can use the final compressed dBG how you like. There are some methods for simplifying and re-building the graph, but those could be developed more.

Examples

• Local phased SV assembly tool in our Long Ranger package
• Single-cell VDJ assember
• Build a colored, compressed dBG of a transcriptome reference

All the data structures in debruijn-rs are specialized to the 4 base DNA alphabet, and use 2-bit packed encoding of base-pairs into integer types, and efficient methods for reverse complement, enumerating kmers from longer sequences, and transfering data between sequences.

Encodings

Most methods for ingesting sequence data into the library have a form named 'bytes', which expects bases encoded as the integers 0,1,2,3, and a separate form names 'ascii', which expects bases encoded as the ASCII letters A,C,G,T.

Modules

clean_graph	DeBruijn graph simplification routines. Currently tip-removal is implemented.
compression	Create compressed DeBruijn graphs from uncompressed DeBruijn graphs, or a collection of disjoint DeBruijn graphs.
dna_string	A 2-bit encoding of arbitrary length DNA sequences.
filter	Methods for converting sequences into kmers, filtering observed kmers before De Bruijn graph construction, and summarizing 'color' annotations.
graph	Containers for path-compressed De Bruijn graphs
kmer	Represent kmers with statically know length in compact integer types
msp	Methods for minimum substring partitioning of a DNA string
test	Generate random genomes (with lots of re-used sustrings), reassemble them, and check sanity
vmer	Variable-length DNA strings packed into fixed-size structs.

Structs

DnaBytes	A newtype wrapper around a Vec<u8> with implementations
DnaSlice	A newtype wrapper around a &[u8] with implementations
Exts	Store single-base extensions for a DNA Debruijn graph.
KmerExtsIter	Iterate over the (Kmer, Exts) tuples of a sequence and it's extensions efficiently
KmerIter	Iterate over the Kmers of a DNA sequence efficiently
MerIter	Iterator over bases of a DNA sequence (bases will be unpacked into bytes).

Enums

Dir	Direction of motion in a DeBruijn graph

Traits

Kmer	Encapsulates a Kmer sequence with statically known K.
Mer	Trait for interacting with DNA sequences
MerImmut	An immutable interface to a Mer sequence.
Vmer	A DNA sequence with run-time variable length, up to a statically known maximum length

Functions

base_to_bits	Convert an ASCII-encoded DNA base to a 2-bit representation
bits_to_ascii	Convert a 2-bit representation of a base to a char
bits_to_base	Convert a 2-bit representation of a base to a char
complement	The complement of a 2-bit encoded base
dna_only_base_to_bits
is_valid_base	Convert an ASCII-encoded DNA base to a 2-bit representation