November 2018
Intermediate to advanced
360 pages
9h 36m
English
Content preview from Bioinformatics with Python Cookbook - Second Edition
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Doing metagenomics with the QIIME 2 Python API
Wikipedia says that metagenomics is the study of genetic material that's recovered directly from environmental samples. Note that "environment" here should be interpreted broadly: in the case of our example, we will deal with gastrointestinal microbiomes on a study of a fecal microbiome transplant in children with gastrointestinal problems. The study is one of the tutorials of QIIME 2, which is one of the most widely used applications for data analysis in metagenomics. QIIME 2 has several interfaces: a GUI, a command line, and a Python API called the Artifact API.
Tomasz Kościółek has an outstanding tutorial for using the Artifact API based on the most well-developed (client-based, not artifact-based) ...