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charles-plessy authored Jul 26, 2024
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**nf-core/pairgenomealign** is a bioinformatics pipeline that aligns one or more _query_ genomes to a _target_ genome, and plots pairwise representations.

<img src= "docs/images/pairgenomealgn-logo.png">
![Tubemap workflow summary](docs/images/pairgenomealign-tubemap.png "Tubemap workflow summary")

The pipeline can generate four kinds of outputs, called _many-to-many_, _many-to-one_, _one-to-many_ and _one-to-one_, depending on whether sequences of one genome are allowed match the other genome multiple times or not.

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