Assemble mystery data in small groups

Make a new directory and unpack the data

mkdir mystery
cd mystery
tar -xvzf /data/mystery_data.tgz

Data QC

As usual, use fastqc to inspect a couple of the samples. Do you see any noticeable features of the data?

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)

Additionally, choose a value for parameter 14 (clust_threshold). This value should be between [0,1], but think about what values make the most sense and why. Try to choose values different from the other groups.

<EXERCISE FOR THE READER>      ## [14] [clust_threshold]: Clustering threshold for de novo assembly

Run the full assembly through step 7 and interpret the results

Regroup and discuss the results of the different clust_threshold values