-
Some users may wish to count kmers from the forward and reverse strands separately. Discussed in #74.
Propose adding an option (stranded/strand_aware?) to make a KmerCountTable store fwd/rev kmers …
-
Hello,
I use `khmer` in `primerForge` to retrieve kmers that appear exactly once in the genome My current workflow is this:
```python
from khmer import Countgraph
def getKmersThatAppearOnce(…
-
oxli is currently slower than other counters for large genomes. Suggest option to bulk load kmer counts from another counter i.e. Jellyfish via text dump.
Would allow users to load pre-calculated c…
-
Hi,
I have encountered another issue.
```
path_to_volcanosv=../VolcanoSV
python3 ${path_to_volcanosv}/bin/VolcanoSV-vc/Small_INDEL/volcanosv-vc-small-indel.py \
-i volcanosv_asm_output_tumor …
-
Hello Jaebom,
I am running into a strange problem using the Refseq Prokaryote/Viral DB to try and classify paired-end short reads. As the run goes on, it just keeps increasing the --match-per-kmer …
-
Hi,
I want to use triocanu for haplotype assembly. For hap1, the expected coverage is 12X on a 0.6G genome (P10), while for hap2, the expected coverage is 21X (P48):
```
canu -p F1_trio -d canu_tri…
-
Hi Dr. Zhang,
Thank you for such a great tool! I am working with a suspected autotetraploid tree species (2n = 4x = 48), and I ran SubPhaser to essentially support it being auto- due to the lack of…
-
Hi, @eblerjana
I found that several samples's peak is wrong according the pangenie log. So would you mind teliing what's the influence of these peak? Is there any way to set peak?
Here is a ex…
baozg updated
2 months ago
-
I'm testing the latest version, and it's increasingly more obvious to me that we'll need to restructure the CLI. Currently it's confusing, and likely not permanent.
Specifically, we need a good str…
-
Hi there Kamil _et al.,_
First off, thanks so much for developing this amazing tool. I am having a pervasive problem with interpreting my smudgeplots - specifically, I am wondering whether they re…