rust-debruijn

De Bruijn graph construction & path compression libraries.

Forked from 10XGenomics/rust-debruijn -- 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.

Notable changes in this fork

• improved memory efficiency
• compact structure for sample labels
• more compact reads containier
• specialized storage for paired reads
• many new summarizing options, including statistical tests and edge coverage
• multithreaded graph constuction and GFA/DOT file writing
• new options for error removal