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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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Allow optional graph normalization #246

Closed AndreaGuarracino closed 1 year ago

AndreaGuarracino commented 1 year ago

Standard workflow:

pggb -i data/HLA/DRB1-3123.fa.gz -p 90 -n 10 -o out1

DRB1-3123 fa gz 3adee61 417fcdf 42e55e5 smooth final og viz_multiqc

Skip graph normalization:

pggb -i data/HLA/DRB1-3123.fa.gz -p 90 -n 10 -o out2 -X

DRB1-3123 fa gz 3adee61 417fcdf 42e55e5 smooth final og viz_multiqc

Do not filter short exact matches:

pggb -i data/HLA/DRB1-3123.fa.gz -p 90 -n 10 -o out3 -X -k 0

DRB1-3123 fa gz 3adee61 692a77d 42e55e5 smooth final og viz_multiqc