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iqbal-lab-org / make_prg

Code to create a PRG from a Multiple Sequence Alignment file
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Input to make_prg #30

Closed khodor14 closed 1 year ago

khodor14 commented 2 years ago

Does the make_prg tool take as input an alignment file of genomes or alignment files of genes? I want to build a graph of E.coli

iqbal-lab commented 2 years ago

Genes (and intergenic regions if you want)

khodor14 commented 2 years ago

So pandora builds a graph from genes not from genomes?

iqbal-lab commented 2 years ago

Yes. This is explained here https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02473-1

leoisl commented 2 years ago

Hello Khodor,

sorry there is not a sample example in this repo that makes understanding the input/output to make_prg easily. We will soon merge a fork that contains new features and also a sample example, but the sample example in the fork also applies to this repo. If it helps, you can find this sample example here: https://github.com/leoisl/make_prg/tree/master/sample_example (but ignore the make_prg update commands, as it is not yet supported in this repo)

cheers

leoisl commented 1 year ago

Closing due to inactivity, feel free to reopen.