-
I'm running STAR-Fusion using the following command:
```
STAR-Fusion \
--left_fq ep_rep1_R1_val_1.fq.gz \
--right_fq ep1_R2_val_2.fq.gz \
--CPU 12 \
--genome_lib_dir /star_fusion/o…
-
[GCF_000392535.3_ASM39253v3_genomic.fna.gz](https://github.com/refresh-bio/KMC/files/2127232/GCF_000392535.3_ASM39253v3_genomic.fna.gz)
For this test_data, which is downloaded from ncbi, we can use k…
-
-
I have a few clarifying questions about the kmer/minimizer stuff because it keeps tripping me up. Correct me if I am wrong, but how I picture the kmer/window size thing working is that a reference gen…
-
Hello,
I gave spacegraphcats another go, and tried to run bits of the code separately so I can understand where things go wrong. This time it's running out of memory at the catlas building phase (s…
-
We should verify that there are parameters that are duplicated with kmtricks, perhaps one filtering (at the beginning) is enough:
- [Minimum count of k-mers to be retained (-c)](https://github.com/…
-
Thanks so much for the Rust implementation and various improvements! Very exciting!
I tried out ska2 v0.3.0 distance and the result is a bit unexpected so trying to understand the difference.
Fre…
-
Currently we have `kmc` as our genome size estimator on TheiaProk suite of workflows. This has shown to be widely inconsistent on ONT data, particularly when very long read sequences are present in th…
-
First of all congratulations for Mash.
After reading the [paper about mash](http://biorxiv.org/content/early/2016/04/19/029827) I decided to try it, and I am really impressed with the good results…
-
Hello,
The samples I am working on are diploid and this is a known fact. However, when I am analysing whole genome short read data the ploidy level on Genomescope result is haploid. What are the …