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https://github.com/broadinstitute/poasta
Fast and exact gap-affine partial order alignment
https://github.com/broadinstitute/poasta
Last synced: 28 days ago
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Fast and exact gap-affine partial order alignment
- Host: GitHub
- URL: https://github.com/broadinstitute/poasta
- Owner: broadinstitute
- License: bsd-3-clause
- Created: 2023-05-29T22:33:58.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-05-28T13:40:45.000Z (7 months ago)
- Last Synced: 2024-05-29T05:29:40.961Z (7 months ago)
- Language: Rust
- Homepage:
- Size: 537 KB
- Stars: 22
- Watchers: 5
- Forks: 0
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-pangenomes - poasta - affine sequence-to-graph and partial order aligner and MSA construction (A list of software capable of analyzing mainly **eukaryotic** genomes for pangenomics. A new section for microbial genomes has also been added, these tools may not scale to large genomes.)
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