Crate debruijn[][src]

Expand description

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.


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.


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.


DeBruijn graph simplification routines. Currently tip-removal is implemented.

Create compressed DeBruijn graphs from uncompressed DeBruijn graphs, or a collection of disjoint DeBruijn graphs.

A 2-bit encoding of arbitrary length DNA sequences.

Methods for converting sequences into kmers, filtering observed kmers before De Bruijn graph construction, and summarizing ‘color’ annotations.

Containers for path-compressed De Bruijn graphs

Represent kmers with statically know length in compact integer types

Methods for minimum substring partitioning of a DNA string

Variable-length DNA strings packed into fixed-size structs.


A newtype wrapper around a Vec<u8> with implementations of the Mer and Vmer traits.

A newtype wrapper around a &[u8] with implementations of the Mer and Vmer traits.

Store single-base extensions for a DNA Debruijn graph.

Iterate over the (Kmer, Exts) tuples of a sequence and it’s extensions efficiently

Iterate over the Kmers of a DNA sequence efficiently

Iterator over bases of a DNA sequence (bases will be unpacked into bytes).


Direction of motion in a DeBruijn graph


Encapsulates a Kmer sequence with statically known K.

Trait for interacting with DNA sequences

An immutable interface to a Mer sequence.

A DNA sequence with run-time variable length, up to a statically known maximum length


Convert an ASCII-encoded DNA base to a 2-bit representation

Convert a 2-bit representation of a base to a char

Convert a 2-bit representation of a base to a char

The complement of a 2-bit encoded base

Convert an ASCII-encoded DNA base to a 2-bit representation