rspoa

POA in Rust

Usage

After cloning the repository from GitHub, move to its main directory and compile the package with cargo build --release To use rspoa you need a .gfa file and a .fasta file containing the reads you want to align to the graph. In order to run rspoa: cargo run --release <reads.fa> <graph.gfa> You can set different parameters and choose between different alignment types: ``` OPTIONS: -h, --help Print help information -V, --version Print version information

I/O: Sequences to align file path Graph file path -o, --out_file Specifies the output file, if not indicated prints in standard output [default: "standard output"]

Alignment: -m, --aln-mode 0: global, 1: local, 2: affine gap, 3: local gap, 4: pathwise alignment[DEMO], -M, --match Match score [default: 2] -X, --mismatch Mismatch penalty [default: 4] -O, --gap-open Gap opening penalty [default: 4] -E, --gap-ext Gap extension penalty [default: 2] -s, --amb-strand Ambigous strand mode, try reverse complement if alignment score is too low [default: false] [possible values: true, false] -t, --matrix Scoring matrix file, if '-t' is used '-M' and '-X' are not used. You should set appropriate gap penalties if aln-mode is 2 or 3[default: none]

Adaptive banded: -b, --extra-b First adaptive banding parameter, set < 0 to disable adaptive banded [default: 1] -f, --extra-f Second adaptive banding parameter, number of basis added to both side of the band = b+f*L, l = length of the sequence [default: 0.01] ```

The output is in .gaf format, in reference to the graph in input.

```

read1 50 0 50 + >1>3>5>6>8>9>11>12>13>15>16>18>19 50 0 11 49 * * 8M,1M,1M,3M,1M,4M,5M,2M,8M,1M,4M,1M,11M ```

Library

rsPOA can also be used as a library for your project. In order to do so add to your Cargo.toml file: [dependencies] rspoa= { git = "https://github.com/AlgoLab/rspoa" } In this case you can use the functions inside the api.rs file, they need only the read as a string and the graph as an HashGraph, other parameters can be set or left by default. You can use them by adding use rspoa::api::* in your file.