Comments (2)
my recommendation would be to rename the input sequences so their naming follows the https://github.com/pangenome/PanSN-spec. The delimiter of choice for PGGB is #
.
You can then use odgi similarity
to calculate a distance matrix based on your species. Telling odgi similarity
that #
is your delimiter of choice, it is able to view several paths as one species. For an example and R code please take a look at https://hackmd.io/@AndreaGuarracino/SyhbiKuE2#Primate-chromosome-6.
However, if you really want some kind of MSA output you can activate a PGGB argument:
-M, --write-maf write MAF output representing merged POA blocks [default: off]
You will get a MAF file for each local MSA in the graph.
I hope this helps!
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I would like to get an answer as well .
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Related Issues (20)
- Converting to a single connected component HOT 2
- vcfwave not found HOT 2
- Construct pangenome HOT 3
- Problems with skipping the wfmash step HOT 8
- Even if the genome is small, shouldn't too many samples be added to build the graph HOT 8
- Wrong setting of POA, but it still finish without error HOT 4
- Path to paf2net.py not correct in latest Docker build HOT 2
- 'SN:Z' and 'SO:i' tags for segments/nodes HOT 1
- How to handle when two contigs from the same assembly sligtly overlap HOT 7
- Construct PanGenome HOT 7
- How to understand the vcf file output by PGGB? HOT 3
- the parameters to build pangenome for metagenomes HOT 2
- [docker] wfmash: error while loading shared libraries: libwfa2cpp.so.0 HOT 1
- --n-haplotypes option not recognized HOT 2
- vg deconstruct error HOT 5
- Command terminated by signal 8 HOT 2
- How to visulize PGGB graph in Sequence Tube Map?
- seqwish fails when `--output-dir` contains commas HOT 1
- Parameters optimization
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