Comments (5)
ekg
commented on August 11, 2024
What happens with default parameters?
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subwaystation
commented on August 11, 2024
docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -n 12 -t 16 -o /data/bi_wfmash_test_1 -M -m
Other fancy graphs.
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subwaystation
commented on August 11, 2024
Alright, I got a nice one with this:
docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 2000 -G 2000 -n 12 -t 16 -o /data/bi_wfmash_test_2 -M -m"
A shorter segment length was required. I am happy now.
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ekg
commented on August 11, 2024
I'd suggest removing -G... that part is very different now. We actually iterate with very short -G three times. So we're just doing very local smoorthing now.
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subwaystation
commented on August 11, 2024
Not sure this helped. The tip of the cavallo seems worse.
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Related Issues (20)
- empty VCF after running PanGenIe on the pggb assembly HOT 1
- GFA with no P lines HOT 5
- PGGB use case with hexaploidy genomes HOT 1
- force reference output in VCF HOT 2
- Three chromosome take too long time HOT 16
- High heterogeneity in sequences identity HOT 2
- extracting node path-coverage information HOT 3
- wfmash -Y option HOT 3
- About the result study HOT 4
- Question about the example "scerevisiae7.fasta.gz " HOT 1
- ValueError: too many values to unpack (expected 13) HOT 3
- Annotating the 1D pangenome graph visualisation with centromere coordinates
- Get the fasta file of non reference sequence
- [W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.) HOT 4
- PGGB get the fasta file of non reference sequence
- Building a graph from fragmented assemblies
- interoperability with vg - error:[vg::SmallSnarlSimplifier] Invalid graph on iteration 0 HOT 14
- Current Bioconda release does not find python scripts HOT 7
- Possible community detection bug HOT 5
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