Bob Literman

The bowtie commands in alignContigs and identifyFixedSites

Looks promising.

Some considerations with respect to the sample dataset, an idea which I wholly agree with: 1) As you stated, small genomes would be great. I'm currently in hour 60 of...

Hi @anderspitman, I wonder if the best way to go with that would be to use a preassembled bacterial genome dataset and a small number of real reads? That way,...

It makes sense to me. Keep in mind I have added options in SISRS to run specific subroutines alone. In that way you could make benchmark datasets for each stage...

If you can give me a few days to get this grant done, I could probably create the data directories relatively quickly, and then you could just clone them all...

I think we're on the same page. I'll look into this more next week.

I gave this a first crack, with some caveats. https://github.com/BobLiterman/SISRS_Small_Data Basics: 1) I took 49 contigs from a primate SISRS run. (Damn header row) 2) Extracted associated reads for 8...

Well, in order to identify biallelic sites you need at least 4 taxa. So in that sense you could reduce it that far and still get all the output. That...

Make raw data (d0), Copy raw folder to dir1, run command 1 in dir1, Copy new dir1 to dir2, Run command 2 in dir2, etc