-
Is it possible to use PhyloCSF on mitochondrial genomes, i.e. with an alternative genetic code?
-
**CHM13V2 T2T Assembly**
```bash
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz
snipe sketch --ref GCF_00…
-
I'm interested in using `mity` to assess within-individual variation in mitochondrial DNA. I have assembled mitochondrial genomes for ~300 individuals of a non-model fish species using `MitoZ` and fou…
-
I'm using getorganelle to extract mitochondrial genomes from insects. I first do an assembly using SPAdes (because we use that output for other downstream tasks anyway), and then I run get_organelle_f…
-
Hi Mike,
I'm a PhD student in Laura Hug's lab currently working on a side project related to constructing universal ToLs. I was following your ToL example using the universal marker gene set and no…
-
Dear author,
Thanks and cheers for developing this package!
I have the question as to how to use the package to download complete mitochondrial genomes from the NCBI. This is because I am going …
-
I wonder if you are interested in developing sketches for mitochondrial or plastic genomes?
-
Hello,
Thank you for creating this great tool. I have successfully run read2tree using marker genes downloaded from OMA browser and my own data, which seems really great.
However, I found some pro…
-
1. Is REGENIE capable of analyzing mitochondrial genomes?
2. If yes, what are the parameters that I need to set to analyze mitochondrial genomes?
-
Hello,
I tried to find the mitochondrial sequences in my assembly.
I assembled CLR PacBio reads using CANU for a mollusc genome.
As reference I used 2 mitochondrial genomes of the same species an…