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spacocha edited this page May 7, 2015 · 16 revisions

SmileTrain: an Alm lab 16S processing pipeline

Introductory material

What is Smile Train?
Getting started
Pipeline overview
Pipeline basics
Common experience & wisdom
Common mistake & gotchas

Tutorials & how-tos

Example workflows
Preflight checks
Converting 3-file input to 2-file input
How to get Greengenes taxonomies
How to process a filtered QIIME fasta

Advanced pipeline topics

Primer removal
Sequence tables
Translating output for oligotyping analysis

For contributors

How to contribute
Code & documentation standards
Adding support for new clusters

Toggle table of contents Pages 17

Home
Adding support for new clusters
Code & documentation standards
Common experience & wisdom
Common mistake & gotchas
Converting 3 file input to 2 file input
Example workflows
Getting started
How to contribute
How to get Greengenes taxonomies
How to process a filtered QIIME fasta
Pipeline basics
Pipeline overview
Preflight checks
Sequence tables
Translating output for oligotyping analysis
What is Smile Train?

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