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aomlomics
Amplicon sequence processing workflow using QIIME 2 and Snakemake
Grant said: I ran into an error on the sequence alignment step, and the culprit was the muscle package. After a little digging, it turns out that a couple of...
While running `snakemake dada2_pe_denoise`, I ran into an error running DADA2. This occurred during the filtering step and was traced back to the version of Matrix in the conda environment...
Command: ``` qiime fragment-insertion sepp ```
Currently supports: ``` Tetramer Amplicon locus Forward primer TACG 16S rRNA prok 515f (EMP) GTAG ITS rRNA euk ITS1f (EMP) GCT[AC] 18S rRNA euk Euk1391f (EMP) GTCG 12S rRNA mt...
Basic workflow: * BLASTN with --outputfmt 11 (ASN) * blast_formatter to get desired format * Ignore "uncultured" hits (by keyword or taxid) * Report NCBI taxomony Code: ``` cd tourmaline/02-denoised/dada2-pe...
Rescript plugin is not currently used in Tourmaline, but is very useful for database formatting and evaluation. Was suggested to include it in the Docker container. https://github.com/bokulich-lab/RESCRIPt/
Not everyone will want to do beta diversityor have extensive metadata, so don't check for that until the diversity step.
config.yaml updates - state that changing database name has no effect on run, just for records - which is done first: trim or trunc? - add newlines for clarity
Getting errors like `invalid escape sequence '\/'`, `invalid escape sequence '\['`, and `invalid escape sequence '\|'` at the start of a snakemake run. May be related to new Python version...