Pangenome validation
Hey, everybody! I'm diving into the topic of pangenome. My team and I have already collected many different variations of the pangenome graph, but I'd like to clarify a couple details. Is there any reliable way how to validate the pangenome graph for adequacy? Maybe pull out some individual complex regions to check or some quality metrics. I'd be happy to have any help.
• 860 views
•
link
updated
by
Uveyik •
•
written
by
aaaniich •
•
written
by
aaaniich •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Constructing a bread wheat pangenome graph using PGGB: per-chromosome vs. whole-genome approach and…
written by Sony Nguyen •
-
Huge discrepancy between Pipseeker & DRAGEN for Pipseq data
written by Arindam •
-
How to interpret and filter vg call output VCF
written by Tobias •
-
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
written by Floren •
-
Right method to annotate genes on pangenome graph
written by Quanyu •
-
Indexing the human pangenome draft
written by lisle.mose •
-
Soft-trim for multistep alignment?
written by TheDurtlerTurtle •
-
vg de novo calling strategy
written by alexis.simon •
-
What to do when transcriptome assembly quality metrics do not concur. How can you decide what assem…
written by MBarcelo •
-
Strategy for genome annotation for a new individual of a well-established species
written by liorglic
Hi, as far as I know, odgi and vg has validation functionality.
odgi validateaccepts .og and gfav1 files, validates the graph checking if the paths are consistent with the graph topology.vg validatecan be used for verification of a gam file.