impg: implicit pangenome graph

Pangenome graphs and whole genome multiple alignments are powerful tools, but they are expensive to build and manipulate. Often, we would like to be able to break a small piece out of a pangenome without constructing the whole thing. impg lets us do this by projecting sequence ranges through many-way (e.g. all-vs-all) pairwise alignments built by tools like wfmash and minimap2.

What does impg do?

At its core, impg lifts over ranges from a target sequence (used as reference) into the queries (the other sequences aligned to the sequence used as reference) described in alignments. In effect, it lets us pick up homologous loci from all genomes mapped onto our specific target region. This is particularly useful when you're interested in comparing a specific genomic region across different individuals, strains, or species in a pangenomic or comparative genomic setting. The output is provided in BED, BEDPE and PAF formats, making it straightforward to use to extract FASTA sequences for downstream use in multiple sequence alignment (like mafft) or pangenome graph building (e.g., pggb or minigraph-cactus).

How does it work?

impg uses coitrees (implicit interval trees) to provide efficient range lookup over the input alignments. CIGAR strings are converted to a compact delta encoding. This approach allows for fast and memory-efficient projection of sequence ranges through alignments.

Using impg

Getting started with impg is straightforward. Here's a basic example of how to use the command-line utility:

impg query -p cerevisiae.pan.paf.gz -r S288C#1#chrI:50000-100000 -x

Your alignments must use wfmash default or minimap2 --eqx type CIGAR strings which have = for matches and X for mismatches. The M positional match character is not allowed.

Depending on your alignments, this might result in the following BED file:

S288C#1#chrI        50000  100000
DBVPG6044#1#chrI    35335  85288
Y12#1#chrI          36263  86288
DBVPG6765#1#chrI    36166  86150
YPS128#1#chrI       47080  97062
UWOPS034614#1#chrI  36826  86817
SK1#1#chrI          52740  102721

In this example, -p specifies the path to the PAF file, -r defines the target range in the format of seq_name:start-end, and -x requests a transitive closure of the matches. That is, for each collected range, we then find what sequence ranges are aligned onto it. This is done progressively until we've closed the set of alignments connected to the initial target range.

Installation

To compile and install impg from source, you'll need a recent rust build toolchain and cargo.

1. Clone the repository:

   git clone https://github.com/pangenome/impg.git

2. Navigate to the impg directory:

   cd impg

3. Compile the tool (requires rust build tools):

   cargo install --force --path .

Authors

Erik Garrison [email protected] Andrea Guarracino [email protected] Bryce Kille [email protected]

License

MIT