SBWT command-line interface

Command-line interface for building, querying, and performing set operations on SBWT (k-mer Spectral Burrows-Wheeler Transform) indexes.

Installation

cargo build --release

The program will be compiled to ./target/release/sbwt. Run the program without any command-line arguments for instructions on how to use it.

Subcommands

Subcommand	Description
build	Build an SBWT index from FASTA/FASTQ input
build-lcs	Build the LCS array for an existing SBWT index
merge	Compute the union of two SBWT indexes
intersect	Compute the intersection of two SBWT indexes
difference	Compute the set difference (index1 \ index2) of two SBWT indexes
jaccard	Compute the Jaccard index of the k-mer sets in two SBWT indexes
lookup	Look up the colex ranks of query k-mers
matching-statistics	Compute matching statistics against an SBWT index
dump-kmers	Print all k-mer strings in colexicographic order
dump-unitigs	Print all unitigs in FASTA format
kmer-at-colex	Print the k-mer at a given colexicographic rank
stats	Print summary statistics of an SBWT index
check	Verify the structural integrity of an SBWT index
benchmark	Benchmark query performance on an index

Citation

If you use this code, please cite the following paper:

@inproceedings{alanko2023small,
  title={Small searchable k-spectra via subset rank queries on the spectral Burrows-Wheeler transform},
  author={Alanko, Jarno N and Puglisi, Simon J and Vuohtoniemi, Jaakko},
  booktitle={SIAM Conference on Applied and Computational Discrete Algorithms (ACDA23)},
  pages={225--236},
  year={2023},
  organization={SIAM}
}