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github.com/10XGenomics/rust-debruijn @v0.3.2

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README

rust-debruijn

De Bruijn graph construction & path compression libraries.

Docs

Key features

2-bit packed fixed-length (Kmer) and variable-length (DnaString) sequence containers
Statically compiled code paths for different K values
Ability to track arbitrary auxiliary data through the DeBruijn graph
Customizable kmer counting & filtering schemes supporting a variety of use cases
DeBruijn graph compression
Minimum-substring partitioning to shard kmers for memory efficient counting and DeBruijn graph compression
Configurable for stranded and non-stranded input sequence
Extensive unit test suite
In production use in Supernova, Long Ranger, Cell Ranger, and Cell Ranger VDJ pipelines from 10x Genomics.

Extension points exported contracts — how you extend this code

KmerSize (Interface)

Helper trait for declaring the K value of a Kmer. Will be removed when const generics are available [15 implementers]

src/kmer.rs

Mer (Interface)

Trait for interacting with DNA sequences [7 implementers]

src/lib.rs

KmerSummarizer (Interface)

Implement this trait to control how multiple observations of a kmer are carried forward into a DeBruijn graph. [2 implementers]

src/filter.rs

CompressionSpec (Interface)

Customize the path-compression process. Implementing this trait lets the user control how the per-kmer data (of type `D` [2 …

src/compression.rs

Array (Interface)

Types that can be used as the backing store for a SmallVec

src/vmer.rs

IntHelp (Interface)

Trait for specialized integer operations used in DeBruijn Graph [5 implementers]

src/kmer.rs

Vmer (Interface)

A DNA sequence with run-time variable length, up to a statically known maximum length [5 implementers]

src/lib.rs

Kmer (Interface)

Encapsulates a Kmer sequence with statically known K. [2 implementers]

src/lib.rs

Core symbols most depended-on inside this repo

Shape

Method 201

Function 96

Class 47

Interface 9

Enum 4

Languages

Rust100%

Modules by API surface

src/kmer.rs73 symbols

src/lib.rs71 symbols

src/dna_string.rs59 symbols

src/graph.rs50 symbols

src/msp.rs25 symbols

src/compression.rs22 symbols

src/test.rs21 symbols

src/vmer.rs13 symbols

src/bitops_avx2.rs10 symbols

src/filter.rs9 symbols

src/clean_graph.rs4 symbols

For agents

$ claude mcp add rust-debruijn \
  -- python -m otcore.mcp_server <graph>

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github.com/10XGenomics/rust-debruijn @v0.3.2

rust-debruijn

Key features

Extension points exported contracts — how you extend this code

Core symbols most depended-on inside this repo

Shape

Languages

Modules by API surface

For agents

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