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gregcaporaso / qiime2-issue190.ipynb
Created Dec 1, 2016
QIIME 2 issue #190 example
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@gregcaporaso
gregcaporaso / qiime-exercise.ipynb
Created Apr 5, 2016
Final assignment for BIO/CS 499/599 (Spring 2016)
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@gregcaporaso
gregcaporaso / notes.md
Last active Nov 10, 2015
convert biom observation counts to per-sample rank abundances
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You'll need to install master of biom-format to use this until the 2.1.6 release is posted (at which point that milestone will be closed, and you can skip this step if you're using biom-format >=2.1.6, < 2.2.0), which you can do as follows:

pip install https://github.com/biocore/biom-format/archive/master.zip

Then, run the following command, substituting your file names for in.biom and out.biom:

python -c "from biom import load_table; t = load_table('in.biom'); t.rankdata(); t.to_json('biom 2.1.5-dev', direct_io=open('out.biom','w'))"
@gregcaporaso
gregcaporaso / notes.md
Last active Mar 28, 2019
vsearch-based sequence dereplication through generation of a biom table
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This depends on biom version >= 2.1.5, < 2.2.0 and vsearch >= 1.7.0.

Please note that all of this is highly experimental. I'm keeping these notes as I work with this approach. For published work, I still recommend using standard pipelines, such as those in QIIME 1.9.1.

$ biom --version
biom, version 2.1.5

$ vsearch --version
vsearch v1.7.0_osx_x86_64, 16.0GB RAM, 8 cores
@gregcaporaso
gregcaporaso / qiime191-or-otus-100-params.txt
Last active Sep 30, 2015
This parameters file can be passed to QIIME 1.9.1's pick_open_reference_otus.py command via the ``-p`` parameter to perform OTU picking at 100% identity. This is a computationally inefficient way to do this, so it may not work with very big data sets. We're working on integrating better approaches.
@gregcaporaso
gregcaporaso / iab-ipynb-to-md.ipynb
Created Jun 17, 2015
Used for gregcaporaso/An-Introduction-to-Applied-Bioinformatics#140 to convert the ipython notebooks to markdown files.
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