-
Hello, Dr. Ahn,
I recently applied TenSQR to reconstruct quasispecies on whole genome sequencing data from a virus sample (>20000X, 150bp paired end, Illumina). TenSQR outputted 10 quasispecies seq…
-
Dear Mr Hirotaka,
We read your paper on this protocol and I was wondering if you had a de-localised form of this repository that could be transferred and used on a different in-house system? We are i…
-
Can we build an option to 'force' permutations? I know we set an upper boundary of 100 which I still think is good - but when recreating a 'quasispecies' and it tells me it'll create 128 permutations…
-
The paper
M. Smerlak, Neutral quasispecies evolution and the maximal entropy random walk. Sci. Adv. 7, eabb2376 (2021)
states: "Data and materials availability: All data needed to evaluate the…
-
Hello, thanks for developing this tool. It looks pretty awesome and I would love to try it out. However, the documentation is not very clear or not present. Is it possible to see a little more documen…
-
Hello, my name is Andrea and I am a bioinformatician who is currently working with SARS-CoV-2 sequences in order to identify quasispecies within given samples. I have been trying to use CliqueSNV so a…
-
Hello!
I was just wondering if this software would be useful to determine full haplotypes or quasispecies in "multiple" CRISPR edited polyclonal mixtures (for example 2 sgRNA's cutting close to each …
-
Dear,
I am very interest in using your tool for my project. I'm working on influenza reads that were sequenced with Illumina MiSeq. I was able to extract quasispecies with LoFreq, however LoFreq do…
-
**Describe the bug**
I am analyzing data from plant (cherry) samples hoping to determine viral quasispecies of Little Cherry Virus
I set up my v-pipe workflow based on the sars-cov2 tutorial
Howeve…
-
Dear developer:
I try to call Quasispecies with a sam file of average depth 200x, and 100%region have a >20X coverage.
however, I found few reads were filled in the covering regions (my refer…