-
First, I'd like to thank you for previous help in getting anvi'o working.
However, now that I can use anvi-refine to improve bins, I realized that I am a bit stuck on the deeper issue of when exact…
-
Hello,
I am having problems with controlling for the population stuctre in my sample set and I was wodnering if I can get some help? I am not sure when the QQplots are good enough in order to be a…
-
@lwaldron, should the values in the Genome_ID column come from a specific source (e.g., PATRIC), or can they come from different sources (both PATRIC and NCBI_ID)? Or should these Ids come from the S…
-
Hi,
I am a relative beginner to bioinformatics. I have assembled 5 30Mbp genomes (of the same species, but different isolates) using nanopore reads with Flye and found really great results. I am no…
-
Hi
I’ve been following your tutorial, using your barley example (http://eead-csic-compbio.github.io/get_homologues/tutorial/pangenome_tutorial.html#41_example_protocol). I’m now parsing the cluster…
-
excuse me:
when I use bam-readcount, I wonder how I can get the region required by bam-readcount? what does this region look like? is it the targeted-region bed file that is provided by vendor?
-
Hello,
I'd like to make sure that I understand how Haystac's alignment works correctly with a custom database. I have a single `genomes.fna` file that contains reference genomes for Bacteria and H…
-
Hello,
I am interested in running a GWAS for a recombinogenic species. Does it make sense to remove recombination from the core tree before running downstream steps? Also is running panaroo with de…
-
Attached find some relevant log files and the run script
[mergelog.txt](https://github.com/jtamames/SqueezeMeta/files/7390210/mergelog.txt)
[syslog.txt](https://github.com/jtamames/SqueezeMeta/fil…
-
Hi,
We have noticed a lack of consistency between Nextclade versions on at least one mutation:
The deletion of nucleotides 22029-22034 on previous versions (tested on 0.12.0 and 0.14.4) is trans…