🍝 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, 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

Install from git

Rust's build tool, cargo supports installing a cli tool straight from github. To do this, simply run the following command. Note that we set the rust compiler flags -C and target-cpu=native to ensure the compiler optimises the build for your CPU. If you wish to make the binary portable, then you can remove these flags.

RUSTFLAGS="-C target-cpu=native" cargo install --git https://github.com/broadinstitute/poasta

This command installs the executables lasagna and poasta that you can access from anywhere (the actual binaries are typically stored in $HOME/.cargo/bin/poasta)

Building POASTA

Alternatively, you can clone the repository and build POASTA that way.

1. Clone the repository.

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

2. Move into the directory.

   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.

   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).

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.

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).

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:

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:

# 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

Gap penalty configuration

POASTA supports both standard affine gap penalties and two-piece affine gap penalties for more flexible gap modeling.

Standard affine gap penalties

By default, POASTA uses standard affine gap penalties with the following defaults:

• Gap opening penalty: 6
• Gap extension penalty: 2
• Mismatch penalty: 4

You can customize these penalties:

poasta align -g 8 -e 3 -n 5 sequences.fasta

Two-piece affine gap penalties

For more sophisticated gap modeling, POASTA supports two-piece affine gap penalties, which use different penalties for short and long gaps. This can better model biological insertion/deletion patterns.

To enable two-piece affine mode, provide comma-separated values for both gap opening and extension penalties:

# Two-piece affine: short gaps (8,2) and long gaps (24,1)
poasta align -g 8,24 -e 2,1 -n 5 sequences.fasta

The first values (8,2) apply to short gaps, while the second values (24,1) apply to longer gaps. The extension penalty for short gaps should be higher than for long gaps to properly model the two-piece behavior.

Alignment modes

POASTA supports different alignment modes:

• global: End-to-end alignment (default)
• semi-global: Query aligned globally, but graph gaps are free at ends
• ends-free: Free gaps at sequence beginnings/ends for both query and graph

poasta align -m ends-free sequences.fasta

Note: Currently, ends-free and semi-global modes are only supported with global alignment.

Related repositories

• poa-bench - Benchmark POASTA against other POA tools
• spoa-rs - Rust bindings to SPOA