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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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Is a way to use minimap2 for pggb #18

Closed XuewenWangUGA closed 2 years ago

XuewenWangUGA commented 4 years ago

Is a way to use minimap2 seqeuence aligner for pggb pipeline? Detailed steps will be very helpful. Thanks.

ekg commented 4 years ago

You'd want to replace the mapping step with it. The first iterations of this pipeline used it.

The only thing that you might want to do is filter the alignments it makes by block length, selecting a length longer than the length of common repeats in the genomes you are working with.

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Is a way to use minimap2 seqeuence aligner for pggb pipeline? Detailed steps will be very helpful. Thanks.

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subwaystation commented 2 years ago

@XuewenWangUGA Is this resolved?

ekg commented 2 years ago

We can support this by taking a PAF in input. I will add this.

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