ilnamkang

theano issue putatively related to the slowdown of the program

5

Hi, When I run DeepVirFinder using multiIcores (e.g. 72 cores), I'm encountering warning messages like below. DeepVirFinder seems to be getting slower with these messages and use only

Documentation website seems to be down

6

Hello, Documentation website (http://enve-omics.ce.gatech.edu/enveomics/docs) seems to be down since at least Christmas holiday of the last year. How can I access to the website? Thanks.

Is "--isolate" option of SPAdes applied to all k-mer sizes?

3

Hi, It seems that the "--isolate" option is used for SPAdes assembly step of Unicycler v0.5.0. I'd like to know whether or not the "--isolate" option is applied to all...

Are there any methods to save the difference between the input and output sequences?

1

Hello, I'd like to save the difference between the input and output sequences (i.e. the changes made by Racon) as a file. Are there any command-line options for this? Thanks.

Thank you for a great tool! Is Pavian dependent on NCBI taxonomy (taxdump files from NCBI)? If not, is it possible to use GTDB taxdump files available at the Struo2...

**Computational environment** - OS: Ubuntu 20.04.1 - CUDA version if Linux Cuda compilation tools, release 12.4, V12.4.131 Build cuda_12.4.r12.4/compiler.34097967_0 ---- Hi, My job failed with an error message like "CUDA_ERROR_ILLEGAL_ADDRESS:...

Hi, Thank you for starting to release the GTDB index for Kraken2. But, the index size is huge to me. Are there any plans to release the capped version of...

Any plan to support X-Mapper as an option for aligner?

1

Hi, I wonder if there is any plan to support X-Mapper as an option for aligner. Gaston, J. M., Alm, E. J., & Zhang, A.-N. (2025). X-Mapper: fast and accurate...

Hi, How can I view a plot showing "Percent of reads" across the samples in the Sankey plot menu available at the Shiny app of Pavian? There is a plot...