This community tutorial has been migrated to our official documentation. Please refer to that tutorial instead.
Click to see original community tutorial
Chimera checking in QIIME 2 is performed on a FeatureTable[Frequency] and FeatureData[Sequences] pair of artifacts. QIIME 2 wraps the Uchime de novo and reference pipelines from vsearch. For details on how these work, see the original Uchime paper, and the vsearch documentation.
This tutorial is designed to work with QIIME 2 2017.12. It may or may not work with other versions of QIIME 2.
In this tutorial, we’ll use the table and sequences from the Atacama soils tutorial.
Download the following files:
Run de novo chimera checking
qiime vsearch uchime-denovo --i-table table.qza --i-sequences rep-seqs.qza --output-dir uchime-dn-out
Note: reference-based chimera checking is also available - see qiime vsearch uchime_ref.
Generate chimera checking summary visualization
qiime metadata tabulate --m-input-file uchime-dn-out/stats.qza --o-visualization uchime-dn-out/stats.qzv
Filter input table and sequences, excluding chimeras and “borderline chimeras”
qiime feature-table filter-features --m-metadata-file uchime-dn-out/nonchimeras.qza --i-table table.qza --o-filtered-table uchime-dn-out/table-nonchimeric.qza
qiime feature-table filter-seqs --i-data rep-seqs.qza --m-metadata-file uchime-dn-out/nonchimeras.qza --o-filtered-data uchime-dn-out/rep-seqs-nonchimeric.qza
qiime feature-table summarize --i-table uchime-dn-out/table-nonchimeric.qza --o-visualization uchime-dn-out/table-nonchimeric.qzv
Filter input table and sequences, excluding chimeras but retaining “borderline chimeras”
qiime feature-table filter-features --m-metadata-file uchime-dn-out/chimeras.qza --i-table table.qza --o-filtered-table uchime-dn-out/table-nonchimeric.qza --p-exclude-ids
qiime feature-table filter-seqs --i-data rep-seqs.qza --m-metadata-file uchime-dn-out/chimeras.qza --o-filtered-data uchime-dn-out/rep-seqs-nonchimeric.qza --p-exclude-ids
qiime feature-table summarize --i-table uchime-dn-out/table-nonchimeric.qza --o-visualization uchime-dn-out/table-nonchimeric.qzv