Sam’s Notebook:Assembly Stats – Quast Stats for Geoduck SparseAssembler Job from 20180405


The geoduck genome assembly started 20180405 completed this weekend.

This assembly utilized the BGI data and all of the Illumina project data (NMP and NovaSeq) with a kmer 101 setting.

I ran Quast to gather some assembly stats, using the following command:

 python /home/sam/software/quast-4.5/ -t 24 /mnt/owl/Athaliana/20180405_sparseassembler_kmer101_geoduck/Contigs.txt 

Quast output folder: results_2018_04_15_13_45_03/

Quast report (HTML): results_2018_04_15_13_45_03/report.html

I’ve embedded the Quast HTML report below, but it may be easier to view by using the link above.


from Sam’s Notebook

Grace’s Notebook: April 15, 2018 Weekly goals

So last week was unfortunately not as productive as I had planned as a result of some dog-sitting shenanigans. So, to help myself get back on top of things, I’m making a list of what I want to and will accomplish this week. Firstly, tomorrow I have a presentation in my FISH 511 class, so I will be focusing on that today and tomorrow. The rest of the week will be as follows:


  • Finish Qubit
  • Finish FINAL RNA isolation of the sub-group of samples I selected a while back. The remaining samples to be isolated are the samples from the three crabs that survived the warm treatment so I cannot mess up.


  • Organize spreadsheets
  • Organize OWL (add READMEs)


  • Continue organization from day before
  • Edit and publish Crab Mtg #2 (S1 Ep 5)


from Grace’s Lab Notebook