# rust-spoa
This crate is a Rust wrapper and interface to the [SPOA](https://github.com/rvaser/spoa) (simd-accelerated partial order alignment) library.
This library allows the efficient generation of a consensus sequence from a set of DNA or protein sequences.
If you use this crate, please cite the original authors of SPOA:
[Vaser, R., Sović, I., Nagarajan, N. and Šikić, M., 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome research, 27(5), pp.737-746.](https://genome.cshlp.org/content/27/5/737)
To use this crate, add the following to your ```Cargo.toml```:
```
[dependencies]
rust-spoa = "*"
```
And add this to your crate root:
```
extern crate rust_spoa;
```
For description of the API, see [the documentation](https://docs.rs/rust-spoa/0.2.4/rust_spoa/):
Example usage:
```
extern crate rust_spoa;
use rust_spoa::poa_consensus;
fn main() {
let mut seqs = vec![];
// generated each string by adding small tweaks to the expected consensus "AATGCCCGTT"
for seq in ["ATTGCCCGTT\0",
"AATGCCGTT\0",
"AATGCCCGAT\0",
"AACGCCCGTC\0",
"AGTGCTCGTT\0",
"AATGCTCGTT\0"].iter() {
seqs.push((*seq).bytes().map(|x|{x as u8}).collect::<Vec<u8>>());
}
let consensus = poa_consensus(&seqs, 20, 1, 5, -4, -3, -1);
let expected = "AATGCCCGTT".to_string().into_bytes();
assert_eq!(consensus, expected);
}
```