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Hi!
I used vg chunk to extract subgraphs from a pan-genome graph and then used vg deconstruct to obtain VCF files for both the pan-genome graph and the subgraph. However, I noticed that the VCF fi…
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I'm querying my .gff files to pull out sequences for certain genes but it is giving me output in amino acids. I saw in a supplementary document that you can get this outputted in nucleotides but the d…
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In the future, I want to map the resequencing data of different species of onto my map genome.Then the group vcf with good classification is used to carry out the process of vgmpmap
I wonder if this …
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Cercis/canadensis/genomes/ISC453364.gnm3.GWXB
- Cercis/canadensis/annotations/IS…
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## The need
Diamond can generate a lot of temporary files. The default /tmp can get full on clusters.
## The solution
Add a parameter `--temp` to the command `anvi-pan-genome`, maybe others t…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Chamaecrista/fasciculata/genomes/ISC494698.gnm1.8Q19
- Chamaecrista/fasciculata…
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Hello, Professor Ou.
Recently, I have been using EDTA to annotate transposable elements (TEs) in multiple animal genomes. However, while some genomes can generate the .mod.EDTA.TEanno.sum file, oth…
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Dear Developer.
I have a question about PGGB pan-genome construction. I hope you can help me answer:
Does PGGB support gradual increase? For instance, by initially building a pan-genome 'Pn' usi…
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Hello, I am using Roary to generate a pan-genome with 682 .gff files obtained from Prokka.
The Roary command I'm using is python3 roary_plot.py --label mytree.newick the tree made by these command is…
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Hello!
When I run the software according to the following code, there is an index error. How can I solve this problem?
Here's my code:
#### step1:build index
scTE_build -g panT…