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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 am running `vg autoindex` to splice the minigraph-cactus full pangenome according to GENCODE v44 gene annotations in order to map RNA-seq reads. I have two questions:
1) By running the follo…
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I used GraphAligner to align HiFi reads of the sample to the HPRC pangenome. The "vg stats" command revealed an alignment percentage of **90.16%** (6056984/6717677). However, upon examining the genera…
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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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I have been running `projection` on a reconstructed pangenome and a set of assembly FastA files for input genomes, in order to assign each gene to a gene family in the pangenome for each input genome.…
szhan updated
1 month ago
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Dear all,
I'm here for the first time in the community and have been trying for some time to obtain a pangenome to use as a reference for mapping short reads using `vg giraffe` and subsequent varia…
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Hi professors!
I have 19 assembly genome of one species,each assembly genome contains 29 chromosomes.I want to construct a graph from the 19 genomes using PGGB. I firstly combine the 19 genome into a…
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In the example below does include.txt need to be a local file or can it point to cloud storage like s3? Thanks!
```
bactopia --wf pangenome \
--bactopia /path/to/your/bactopia/results \
--i…
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Hello! Out of curiosity, in the description of the pipeline you say that "Struo2 is designed to process one genome representative of each species, which is all that is required for generating the Krak…
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**Description**
I was able to run the main pipeline, I used bakta as an annotator instead of prokka
I am not able to run neither summary command or the pangenome workflow using panaroo. I think it…