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https://github.com/broadinstitute/poasta

Fast and exact gap-affine partial order alignment
https://github.com/broadinstitute/poasta

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Fast and exact gap-affine partial order alignment

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README 

        
🍝 POASTA


Fast, gap-affine sequence-to-graph and partial order aligner



 



POASTA is a fast and optimal partial order aligner that supports gap-affine alignment penalties. Inspired by 

a recent [algorithm for pairwise alignment](https://github.com/smarco/WFA2-lib), it can exploit exact matches

between the query and the graph, greatly speeding up the alignment process.



## Installation



### Pre-built binaries



TODO



### Conda



TODO



### Building POASTA from source



#### Rust compiler



POASTA is written in Rust, and to build and install it, you'll need a recent version of the Rust compiler. The 

minimum supported Rust version is 1.70.



1. Download and install `rustup`: https://rustup.rs/

2. Run `rustup update`



#### Building POASTA



1. Clone the repository. 

    

   ```bash

   git clone https://github.com/broadinstitute/poasta

   ```

 

2. Move into the directory. 



   ```bash

   cd poasta

   ```

 

3. Build using `cargo`. We enable a flag to ensure the compiler uses all features of your machine's CPU. 

   To maximize portability of the binary, however, remove the `RUSTFLAGS="..."` part.

    

   ```bash

   RUSTFLAGS="-C target-cpu=native" cargo build --release

   ```

 

4. The built `poasta` executable will be available in the directory `target/release/`



## Usage



### Creating an alignment from scratch



To create a multiple sequence alignment from scratch, simply give it a FASTA. The FASTA file can be compressed 

with gzip (filename should have a `.gz` extension).



```bash

poasta align -o graph.poasta sequences.fasta

```



This will output the graph to a binary file called `graph.poasta`. POASTA can reuse this file to later align

additional sequences to it.



### Re-using an earlier alignment



To align additional sequences to an earlier created partial order graph, specify the existing graph using the 

`-g` option.



```bash

poasta align -g graph.poasta -o graph_updated.poasta new_sequences.fasta

```



This will import the graph stored in `graph.poasta`, then align the additional sequences in `new_sequences.fasta` to

this graph, and outputs the updated graph to `graph_updated.poasta`.



### Importing an existing multiple sequence alignment in FASTA format



POASTA can import an existing multiple sequence alignment stored in columnar FASTA format (e.g., those 

created by other tools like `mafft` or `spoa`), create the equivalent partial order graph from the existing alignment,

and then align new sequences to it. To achieve this, specify the FASTA MSA with extension .fa, .fna, or .fasta with

the `-g` option (file is also allowed to be compressed with gzip if it has a `.gz` suffix).



```bash

poasta align -g msa.fasta -o graph_updated.poasta new_sequences.fasta

```



### Other output formats



The default output format is POASTA's binary file format storing the graph data structure.

This the recommended output because you can always convert this binary file

to other formats using `poasta view`.

If you don't need the binary file, however,

you can specify the output format with the `-O` option:



Other supported formats:



* DOT (GraphViz): Specify with `-O dot`

* FASTA MSA: Specify with `-O fasta`

* Graph GFA: Specify with `-O gfa`



For example, to visualize the graph directly with GraphViz:



```bash

poasta align -Odot sequences.fasta | dot -Tpng -o graph.png

```



Note that we did not specify an output file for `poasta align` (we did not use the `-o` option). If no output filename

is given, standard output will be used, so the output can be directly piped to `dot` to create the visualization.



### Using `poasta view` to convert between output formats



By default, POASTA stores the computed graph/MSA in its own binary file format.

To convert a previously computed MSA to other file formats, you can use `poasta view`.

The supported output formats are the same as described above, i.e.:



* DOT (GraphViz): Specify with `-O dot`

* FASTA MSA: Specify with `-O fasta`

* Graph GFA: Specify with `-O gfa`



Example:



```bash

# Convert to GFA

poasta view -Ogfa existing_msa.poasta > poa_graph.gfa



# Convert to FASTA MSA

poasta view -Ofasta existing_msa.poasta > poa_msa.fasta

```



## Related repositories



* [poa-bench](https://github.com/broadinstitute/poa-bench) - Benchmark POASTA against other POA tools

* [spoa-rs](https://github.com/broadinstitute/spoa-rs) - Rust bindings to SPOA