Assemble mystery data in small groups

Launch a new ipyrad binder instance

• Launch ipyrad with binder.

Make a new directory for the mystery assembly

mkdir mystery
cd mystery

Download the data to your computer and upload it to binder

• Download the mystery data from wetransfer (15MB)
• Change to the mystery directory in the file browser (on the left)
• Choose the upload (up arrow) button and upload the mystery_data.tgz file
• Unpack the mystery_data.tgz like this:

  tar -xvzf mystery_data.tgz
  

Create a new params file and modify at least these four parameters

We will give you parameters 7, 8, and 25 (because they will be hard to figure out) but you need to figure out what to put for parameter 4 by yourself :)

<EXERCISE FOR THE READER>      ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files
ddrad                          ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc.
CAATTC, TTA                    ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2)
0, 50, 0, 0                    ## [25] [trim_reads]: Trim raw read edges (R1>, <R1, R2>, <R2) (see docs)

Run the full assembly through step 7 and interpret the results

• And have fun ;)

Smaller dataset

If that 15MB dataset is too large and runs too slow you can try this one:

7MB mystery dataset on wetransfer