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• compressed all sample_fastq/ files with pigz: using sbatch /project/microbiome/data/seq/HMAX1/demultiplex/run_pigz.sh

• moved fastq for all four blank samples (data are all in one file because names are collapsed; noted above) to a subfolder (/project/microbiome/data/seq/HMAX1/demultiplex/sample_fastq/blanks), to get them out of the way.

• worked on getting denovo assembly startedstarted denovo assembly in /gscratch/buerkle/data/HMAX1/denovo Completed first step for dDocent. cd-hit-est next.

To do:

• Do de novo assemblies

• Summarize the parse report files in /gscratch with some code to iterate over all the individual reports and get an overall count.

• variant calling

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