msbwt2

The intent of crate is to provide Rust functionality for querying a Multi-String BWT (MSBWT), and is mostly based on the same methodology used by the original msbwt.

NOTE: This is very much a work-in-progress and currently only being updated as a side project during spare time. If you have any feature requests, feel free to submit a new issue on GitHub. Here is a current list of planned additions:

Incorporate the high-memory BWT implementation from fmlrc2
Add a built-in BWT construction tool (instead of relying on external tools like ropebwt2)
Add some more query functionality

Installation

All installation options assume you have installed Rust along with the cargo crate manager for Rust.

From Cargo

cargo install msbwt2
msbwt2-convert -h

From GitHub

git clone https://github.com/HudsonAlpha/rust-msbwt.git
cd rust-msbwt
#testing optional
cargo test --release
cargo build --release
./target/release/msbwt2-convert -h

Usage

MSBWT Building

The Multi-String Burrows Wheeler Transform (MSBWT or BWT) must be built prior to performing any queries. Currently, there is no built in builder, but we expect to have one included soon. For now, the original instructions can be used.

Given a FASTQ file of reads (reads.fq.gz), you can also use the following command from this crate to create a BWT at comp_msbwt.npy.
Note that this command requires the ropebwt2 executable to be installed:

gunzip -c reads.fq.gz | \
    awk 'NR % 4 == 2' | \
    sort | \
    tr NT TN | \
    ropebwt2 -LR | \
    tr NT TN | \
    msbwt2-convert comp_msbwt.npy

Optional Construction Speedup

If you are only using the BWT for k-mer queries, then the sort can be removed from the above command. This will reduce construction time significantly, but loses the read recovery property of the BWT.

Queries

The general use case of the library is k-mer queries, which can be performed as follows:

use msbwt2::msbwt_core::BWT;
use msbwt2::rle_bwt::RleBWT;
use msbwt2::string_util;
let mut bwt = RleBWT::new();
let filename: String = "test_data/two_string.npy".to_string();
bwt.load_numpy_file(&filename);
assert_eq!(bwt.count_kmer(&string_util::convert_stoi(&"ACGT")), 1);

Reference

msbwt2 does not currently have a pre-print or paper. If you use msbwt2, please cite the one of the msbwt papers:

Holt, James, and Leonard McMillan. "Merging of multi-string BWTs with applications." Bioinformatics 30.24 (2014): 3524-3531.

Holt, James, and Leonard McMillan. "Constructing Burrows-Wheeler transforms of large string collections via merging." Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 2014.

License

Licensed under either of

Apache License, Version 2.0 (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)

at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.

msbwt2 0.1.0