Lack of documentation

[jweger1988]

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 documentation on how to run quasitools complexity for example? Thanks in advance for your help.

[emarinier]

Hello,

Sorry about the lack of documentation. It's something that we're starting to work on now.

The complexity tool reports quasispecies complexity measures recommended by Gregori et al. 2016.

Currently, the tool takes a single, aligned, FASTA file as input and reports the measures of complexity to the output. After quasitools is installed, you can run the complexity command as follows:

quasitools complexity aligned.fasta

[jweger1988]

Hey,

Thanks for the quick reply. So the input would be the output of some haplotype calling program then? It doesn't appear quasitools has a haplotype calling function, or am I missing it? Thanks again.

[emarinier]

No, I don't believe there's any other quasitools tool designed to work directly with the complexity tool.

One situation where this tool might be useful is if you have sequencing data of a particular region, perhaps a portion of the Pol gene in HIV, and you want to understand the quasispecies complexity of that region. You might align the reads to a reference (using Bowtie2, or similar) and organize them into an (aligned) FASTA file and use that as input to complexity.