-
I have had kraken2 standard installed for a couple of years and have used it with no issues. I would like to add fungal identification to my analysis, so I would like to replace the standard kraken2 …
-
Hello,
I am running `bcalm` as part of the spacegraph cats pipeline in collaboration with @taylorreiter. The command I am running is: `bcalm -in INFILES -out OUTFILE -kmer-size 31 -abundance-min 1…
-
Hi,
In the latest version 1.38 when I am running Somatic-WGS workflow, it is expecting a ploidyVcfFile at the 5th step 'CanvasPartition'.
So the command has:
${DOTNET}/dotnet {$CANVAS}/CanvasPa…
-
I would like to adjust the repeat time for analyzing the reads. In 'deep simulator 1.0' paper as attached in the pdf, there is a parameter in page number 7 called 'a' for adjusting. But I couldn't fin…
-
Thanks for this nice too! Does this tool also work for binning eukaryotic MAGs?
-
I love your tool. Thanks for making it.
I am using it with a collection of WGS Shigella isolates and some of the plasmid descriptions have multiple hits on NCBI. Is there a way I can figure out w…
-
# spacegraphcats read indexing
with sgc, we need to be able to go from k-mer to cDBG unitig to read. How is this implemented?
First, we put all of the reads in a BGZF file, which is a gzipped fi…
-
At the moment kevlar is painfully slow. We've been philosophizing for a while now whether this was more likely due to the poor cache locality of khmer's Count-Min Sketch implementation or to slow Fast…
-
Dear Writer !
Thanks for your useful pipline, but I meet an error when use SubPhaser.
My command
`subphaser -i groups_genome.fasta -c groups_sg.config`
My configue file
![image](https…
-
Hi, I keep getting the above error:
`ERROR: Could not find .aligned.fa/.vcf in PC0086b-S0390
make: *** [Makefile:108: core.aln] Error 2
make: *** Waiting for unfinished jobs....
make: Leaving dir…