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Hi
I have a question in regards to how VG handles repeat regions.
My genome is around 80% repeats, based on some papers I've read and my results with Repeat Masker.
I'm working with a 20 geno…
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**Assignee:** Ali Haider Bangash
The first step is to identify what data could be integrated through a knowledge graph and what is available. What did the other Hackathon teams accomplish? What is …
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Dear all,
We already have constructed a graph from six genomes (five newly assemblied genomes plus one backone reference). I want to focus on the non-backone references added in the graph. Can I us…
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I'm thinking of doing the command line for this snakemake app differently; right now I'm not using config files much, just the sample name. How does the below sound?
each command would be successiv…
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Hello,
First of all: thank you very much for the pipeline.
I ran the command like this:
nextflow run cgroza/GraffiTE --assemblies assemblies.csv --TE_library nrTREP20 --reference Bgt_genome_v…
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Is strobealign a good basis for the following application:
We would align against a pangenome FASTA. So we might have 100 genomes in this system. Downstream we project the alignments into a graph f…
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Hello!
I address you because I want to perform a little experiment using graphs. I would like to make a string graph from several similar reference genomes. Once made, I would like to convert the str…
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Dear author,
Thank you for developing such a milestone software, which greatly accelerates the efficiency of assembly.
I am currently conducting assembly of a large genome of a plant species, whi…
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Hi,
Firstly, I've built a pangenome from 14 genomes. I've used our genome of reference to align the reads and extract the .fasta file from alignment resulting .bam combining these 14 genomes (.fast…
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Hello,
I want to know if I have some de novo genomes to build a graphical pangenome, except the recommended method [https://github.com/pangenome/pggb](url), whether the `minigraph` [https://gith…