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Published 20 hours ago • verified publisher icon aomlomics
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Amplicon sequence processing workflow using QIIME 2 and Snakemake

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Add functionality for Tronko taxa assignment

https://elifesciences.org/articles/85794 https://github.com/lpipes/tronko

ksilnoaa avatar ksilnoaa

Version 2

How to prevent Snakemake from re-running rules when their output is already present

Snakemake has the unfortunate habit of re-running rules when their output is already present. To prevent this, follow these steps: 1. Run the rule you want with the `--dry-run` flag....

lukenoaa avatar lukenoaa

Write script to iterate through parameters and do multiple Tourmaline runs

This could be implemented in the main tourmaline.sh script, like with another option. Or it could be external and designed with HPC in mind. Would be nice to also include...

ksilnoaa avatar ksilnoaa

Try out V2 workfllow with newest qiime2 version.

ksilnoaa avatar ksilnoaa

Write rules for dada2 SE and deblur

In file `repseqs_step.Snakefile`

ksilnoaa avatar ksilnoaa

Incorporate BLCA from Anacapa as a taxonomy option

Adapt code from here: https://github.com/limey-bean/Anacapa/blob/New-Master/Anacapa_db/scripts/blca_from_bowtie.py

ksilnoaa avatar ksilnoaa

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Amplicon sequence processing workflow using QIIME 2 and Snakemake

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