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@gregcaporaso
gregcaporaso / assignment-5.ipynb
Last active Aug 29, 2015
BIO/CS 290, BIO 599 Assignment 5: Spring 2015
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@gregcaporaso
gregcaporaso / pynast-reference-comparison.ipynb
Last active Aug 29, 2015
Comparison of using GG 13_8 versus Greengenes core set as the default reference for PyNAST
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@gregcaporaso
gregcaporaso / 180-dev.ipynb
Created Nov 6, 2014
comparison of runtime for single_rarefaction.py in QIIME 1.8.0 and 1.8.0-dev
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gregcaporaso / neighbor-joining-experiments.ipynb
Created Jun 11, 2014
initial experiments with implementing neighbor joining for scikit-bio
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@gregcaporaso
gregcaporaso / simple-illustration.ipynb
Last active Aug 29, 2015
taxa collapsing discrepancy
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@gregcaporaso
gregcaporaso / README.md
Last active Aug 29, 2015
quick-and-dirty sortmerna-based consensus taxonomy assigner
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This is a first pass at doing rRNA read assignment with sortmerna. This code is completely untested, but provides the framework for starting to test this as an alternative to QIIME's existing taxonomy assigners.

To use this code you'll need:

  • QIIME 1.8.0 or later
  • scikit-bio (latest GitHub version)
  • The sortmerna binaries in your PATH environment variable.
git clone https://gist.github.com/10506167.git smr-tax
@gregcaporaso
gregcaporaso / README.md
Last active Aug 29, 2015
exploring using pandas for QIIME mapping files
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Some exploration into how the pandas DataFrame could be a useful underlying representation for QIIME's metadata mapping files.

@gregcaporaso
gregcaporaso / variability_v_diversity.py
Last active Aug 29, 2015
first pass script for comparing median diversity versus median variability for a given category
View variability_v_diversity.py
#!/usr/bin/env python
# File created on 26 Feb 2014
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2014, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Greg Caporaso"
@gregcaporaso
gregcaporaso / check_illumina_barcodes.py
Created Dec 3, 2013
Script for performing some basic testing on Illumina amplicon sequencing primers as described in: http://www.nature.com/ismej/journal/v6/n8/full/ismej20128a.html
View check_illumina_barcodes.py
#!/usr/bin/env python
# File created on 01 Dec 2011
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.3.0-dev"
__maintainer__ = "Greg Caporaso"
View fq_qual.py
#!/usr/bin/env python
from sys import argv
from random import random
from cogent.parse.fastq import MinimalFastqParser
from cogent.draw.distribution_plots import generate_box_plots
from qiime.quality import ascii_to_phred33
from qiime.util import qiime_open
def fastq_quality_plots(fastq_records,
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