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When I use `.vg` graph in GraphAligner's mapping command `GraphAligner -g chr21.vg -f chr21.fq -t 88 -a graphaligner_aln.gam -x vg,` there is something error:
![image](https://github.com/maickrau/Gra…
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I'm very sorry to bother you
Recently, I choosed alt contigs on a chromosome to construct a pangenome.
When I used a gbz file constructed by minigraph cactus, gencode. v38. primary.gff, and alt.…
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The error log file as:
[E::bgzf_uncompress] inflate failed: invalid distance too far back
[E::bgzf_read_block] inflate_block error -1
Number of samples in line and header disagrees at chr2:13176554…
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Hi
I'll be starting a new pangenome project shortly and was wondering if anyone had any advice on how to go about generating a pangenome graph from a hexaploidy genome.
Previously with a diploid…
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Hello,
I generated a pangenome graph using 16 haplotypes, and would like to use the default graph (rather than allele freq. filtered graph) for read mapping with giraffe.
However, when I check t…
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Hi,
I found [Panache](https://github.com/SouthGreenPlatform/panache) a web-based interface designed for the visualization of linearized pange…
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Dear all,
When generating graph genome according to the pipeline https://github.com/pangenome/HPRCy1, I found that some long assembled contigs (generated using hifisam) can not be aligned to the re…
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Hi there,
As shown in the paper of seqwish, the genome graph induced by wfmash+seqwish is unbiased, i.e., the graph will not be changed by the order of input genomes. However, a recent paper, "Com…
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Hi!
I found this error (Command terminated by signal 9) when running PGGB, which may be caused by insufficient memory.
I want to know how much memory is needed if I want to use PGGB to construc…
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Hi,
I apologize in advance for the lack of code examples but I have to estimate computational resources before starting the project and I was hoping to get some guidance.
We are working on a complex…