gregcaporaso / README.md

Last active December 19, 2015 05:18

Code for demultiplexing fastq data where index reads and barcodes are included in the beginning of sequences. This code depends on QIIME 1.7.0.

To run this code and pass the results into split_libraries_fastq.py:

prep_sl_fastq.py -b AmpF_25k.fastq.gz -m mapping.txt -o prepped_fastq
cd prepped_fastq
split_libraries_fastq.py -i AmpF_25k.fastq.amplicon.fastq -b AmpF_25k.fastq.barcode.fastq -m ../mapping.txt -o slout/ --barcode_type 12

gregcaporaso / README.md

Last active December 18, 2015 10:39

Hack for converting TGEN SNP pipeline output into files that can be converted to BIOM format for analysis with QIIME.

This is all UNTESTED CODE!!

Description

This software allows users to convert TGEN SNP tables to legacy-formatted QIIME OTU tables, which can then be converted into BIOM tables with convert_biom.py (from the biom-format package). This was quickly hacked together, so is untested, but intended to be useful in figuring out if making these tables available in BIOM format will support useful analyses.

Install

gregcaporaso / generate_sample_ids.py

Created May 29, 2013 20:26

Generate sample ids for the office surface succession project.

	#!/usr/bin/env python
	# File created on 29 May 2013
	from __future__ import division

	__author__ = "Greg Caporaso"
	__copyright__ = "Copyright 2011, The QIIME project"
	__credits__ = ["Greg Caporaso"]
	__license__ = "GPL"
	__version__ = "1.6.0-dev"
	__maintainer__ = "Greg Caporaso"

gregcaporaso / clean_nifH_tax.py

Created May 7, 2013 19:23

A single-use script for cleaning up taxonomy strings from a nifH database generated by Gady and Buckley (2012) and exported by the authors from ARB. This is being use to hack together a 13_5 release of a nifH database for use with PrimerProspector and QIIME. The database reference is: PLoS One. 2012;7(7):e42149. doi: 10.1371/journal.pone.0042149…

	#!/usr/bin/env python
	# File created on 07 May 2013
	from __future__ import division

	__author__ = "Greg Caporaso"
	__copyright__ = "Copyright 2011, The QIIME project"
	__credits__ = ["Greg Caporaso"]
	__license__ = "GPL"
	__version__ = "1.6.0-dev"
	__maintainer__ = "Greg Caporaso"

gregcaporaso / README.md

Last active December 15, 2015 20:58

Experimental wrappers for usearch 6.1. None of this is tested - just playing.

Closed-reference OTU picking:

usearch61 -usearch_global seqs.fna -db refseqs.fasta -id 0.97 -uc usearch_global.uc -strand both

De novo OTU picking:

gregcaporaso / otu_table.biom

Last active December 15, 2015 18:59

biom-format issue #120 example files

{"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Staphylococcaceae"]}}, {"id": "1", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "2", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "3", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "4", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "5", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "6", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "7", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmic

gregcaporaso / biom_subsampled_replicates.py

Last active December 15, 2015 04:59

A quick script to generate a table of samples derived by subsampling each sample of a larger BIOM table c times to n sequences per sample.

	#!/usr/bin/env python
	# File created on 20 Mar 2013
	from __future__ import division

	__author__ = "Greg Caporaso"
	__copyright__ = "Copyright 2011, The QIIME project"
	__credits__ = ["Greg Caporaso"]
	__license__ = "GPL"
	__version__ = "1.6.0-dev"
	__maintainer__ = "Greg Caporaso"

gregcaporaso / bad_otu_table.txt

Created March 20, 2013 15:34

An example of an OTU table that gives an annoying biom-format error.

	#OTU ID s1 s2 s3
	1 1 1
	2 1 1 1
	3 1 1 1

gregcaporaso / template_cl_interface.py

Last active December 15, 2015 03:49

A template that can be used as I work on QIIME issue #774: https://github.com/qiime/qiime/issues/774

	#!/usr/bin/env python
	from __future__ import division

	__author__ = "Greg Caporaso"
	__copyright__ = "Copyright 2013, The QIIME project"
	__credits__ = ["Greg Caporaso"]
	__license__ = "GPL"
	__version__ = "1.6.0-dev"
	__maintainer__ = "Greg Caporaso"
	__email__ = "gregcaporaso@gmail.com"

gregcaporaso / trim_mirna_adapters.py

Last active December 14, 2015 15:49

A very quick-and-dirty, untested script to see if it'll be possible to analyze miRNA sequence data in [QIIME](www.qiime.org). Just need this code to perform some initial sequence processing. THIS SCRIPT IS UNTESTED - DO NOT USE FOR ANYTHING IMPORTANT!!!

	#!/usr/bin/env python
	# File created on 07 Mar 2013
	from __future__ import division

	__author__ = "Greg Caporaso"
	__copyright__ = "Copyright 2011, The QIIME project"
	__credits__ = ["Greg Caporaso"]
	__license__ = "GPL"
	__version__ = "1.6.0-dev"
	__maintainer__ = "Greg Caporaso"

Greg Caporaso gregcaporaso

Description

Install