Work as a team to QC and potentially assemble the genomes you’re given. Split up tasks between you, for example, one person run FastQC, another runs KAT hist, another runs KAT gcp, and another runs Kraken.
Keep a record of what you have done, and present the results of your analysis at the end of the session.
Your task is, as a team, to do quality control of the reads. Start off by subsampling the reads to a managable size, say 10%, of the total reads. Because of the size of the genome, it is unlikely that you will have time assemble the genome, but you are welcome to try if you find the time. Do you find any problems with the data?
The reads can be found in the folder:
/proj/g2017025/exercises/Diatom_Assembly_Project
Your task is, as a team, to investigate the data and find out why the Yeast is not assembled well. Focus on quality control, but if you have time you can try to assemble the genome also.
The reads can be found in the folder:
/proj/g2017025/exercises/Yeast_assembly
Your task is, as a team, to quality check the data and then assemble it as best you can. How useful are these data for assembly? Which assembler gives you the best result?
/proj/g2017025/exercises/Bacteria_assembly