Running a test assembly on a subset of data

Choosing a subset

We decided to choose 5 individuals from each of the four locations and start the test assemblywith 20 individuals. The selected individuals can be found in Assembly_subset_round1.csv uploaded separately.

dDocent Assembly

The files for the chosen subset was copied into a new dir called round1/RefOpt housed in the /home/tejashree/Moorea/ddocent/ dir. dDocent was run allowing trimming, type of assembly PE, clustering similarity 0.85%, Minimum within individaul coverage level to include a read for assembly (K1) = 3, Minimum number of individuals a read must be present in to include for assembly (K2) also as 3 since this was the value right before the asympote for both plots. The rest of the parameters were chosen as defaults.

The log file /home/tejashree/Moorea/ddocent/round1/ReOpt/dDocent.runs has all the chosen parameters for this run.

dDocent assembled 76568 sequences (after cutoffs) into 26666 contigs