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I want to generate a VCF file from haplotype-resolved assemblies using pangenome-graph-from-assemblies, recommended in document, but encounter error. Is it a format problem of config.json ? The pictur…
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Kind of like bandage mixed with current plots
Use would be to determine HGT and resolve contigs with highly different coverage
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Hi,
I've generated the graph VCF (results/multisample-vcfs/graph-filtered.vcf) from assemblies by running the [pangenome-graph-from-assemblies](https://bitbucket.org/jana_ebler/pangenome-graph-from…
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```
Then, the circular contigs were left alone, and each tangled “circle” was re-assembled by Hifiasm-meta with default parameters, using the fragmental contigs that constructed the “circle” as input…
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Hi @voutcn and @aquaskyline,
I ran megahit 1.2.9 and got the following graph with `megahit_toolkit contig2fastg 141 final.contigs.fa`:
![image](https://github.com/voutcn/megahit/assets/10245822/c3…
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Hello Vini,
I got a have been using MetaCoAG for a while, works well most of the time until I got a `KeyError: contig_4488`. The dataset Ive been working on is ONT, assembled on metaFlye.
This c…
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Hi, Could you point me to the baseline code to extract "chain of bubbles" from assembly graph? Also, I am not sure about the complete algorithm to simplify graph to extract chain of bubbles, is it we …
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Hi, anyone is interested in aligning PacBio reads to assembly graph? I tried few examples, it looks vg does not do the right thing. Here are the listed things:
1. align pacbio reads to assembly (base…
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Hi @ctb
I believe it was in your blog post on spacegraphcats that you mentioned that basically all metagenomic assembly graphs are connected, and thus an approach based on graph cuts would not wor…
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Hello,
With Verkko 2.2, we get T2T length sequences for nearly all the chromosomes for our sample. However, we noticed that for chromosome 9, the assembly phasing was actually worse. Previously usi…