-
Hi,
My name is Maggs. We recently generated a pangenome graph. We used soft-masked genomes as input. Since then, we revised the masking. The regions that are soft masked differ rather substantiall…
-
Hi,
I have a design question. My initial reaction to the concept of bactopia-tools and how each subworkflow essentially becomes its own, separate (manual!) command line call was one of "uhm why?!".…
-
Hi, When I want to build a 30 species pangenome database for snp calling, I meet some errors. fna and other files were downloaded from PATRIC database. I found that some of strain's fna files failed …
-
Hi,
I am running the step-by-step pangenome pipeline and failed at `filter_paf_deletions` in `cactus-graphmap`
Based on this log `Exit reason: MEMLIMIT`, it should be caused by insufficient memo…
-
I have performed the bacterial pangenome analysis using your pipeline. But, I do not know how to obtain/calculate the Heaps Alpha value from the analysis result, to know the pangenome is open or close…
-
Dear Professor Hukang,
I am delighted to see that your work has developed a pipeline capable of accurately identifying full-length TEs. I have also been troubled by the overly fragmented TEs annot…
-
Hi,
I am having the following issue. Any help will be appreciated.
A problem with the BLAST results file /primerdesign/Lactobacillus_curvatus/Pangenome/results/primer/primerblast/primer_0_result…
-
Make a "quick start" section in the main README file and move demonstrations of more complicated analyses to a GitHub wiki.
Example of a more complicated analysis to explain in the wiki: creating …
-
**1. What were you trying to do?**
Call variants from read support.
**2. What did you want to happen?**
Generate a VCF file.
**3. What actually happened?**
The command have been running…
-
Hi !
I have followed the **Minigraph-Cactus Pangenome Pipeline** to construct a graph-based pangenome and output the index using Giraffe. Additionally, I have used Giraffe to perform read mapping f…