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Status (9 28 February 2021)
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These are the informatics for the Bioinformatics iSeq100 Pilot1 library prep.
Demultiplexing and splitting
...
module load swset/2018.05 gcc/7.3.0 usearch/10.0.240
./aggregate_usearch_fastx_info.pl
See summary_sample_fastq.csv for read counts for each sample.
Trim, merge, and filter reads
Using the current steps in Bioinformatics v3.0, we trimmed primers from reads with cutadapt, and merged and filtered them with vsearch. Output is in /project/microbiome/data/seq/gtl_tests/iSeq100Pilot1_brew_30nov20/tfmergedreads, which is further broken by 16S and ITS, and project name.
Within each of these directories are files for the trimmed, merged, and filtered reads. In each of these directories, there are subfolders trimmed/, joined/, and unmerged/ (the last one is used as a working directory, should be empty; unmerged reads are filtered and joined and put in joined/ if they can be joined; the joined directory can be empty, if all unmerged reads were coligos for example). For example, see contents of /project/microbiome/data/seq/gtl_tests/iSeq100Pilot1_brew_30nov20/tfmergedreads/16S/brew_20/
Make OTU table
In /project/microbiome/data/seq/gtl_tests/iSeq100Pilot1_brew_30nov20/otu, I ran run_slurm_mkotu.pl, which I modified to also pick up the joined reads (in addition the merged reads). On I reran this with a modification to correctly and unique label (assign names to) otus in the table that is used as a database for otutable generation. These jobs should be complete later on .