# Identifying and filtering chimeric feature sequences with vsearch
**URL:** https://forum.qiime2.org/t/identifying-and-filtering-chimeric-feature-sequences-with-vsearch/2252
**Category:** Tutorials
**Tags:** chimera, preview, vsearch, tutorial
**Created:** [December 17, 2017, 2:22pm UTC](https://forum.qiime2.org/t/identifying-and-filtering-chimeric-feature-sequences-with-vsearch/2252 "2017-12-17T14:22:05Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [December 17, 2017, 2:22pm UTC](https://forum.qiime2.org/t/identifying-and-filtering-chimeric-feature-sequences-with-vsearch/2252/1 "2017-12-17T14:22:05Z")
This community tutorial has been [migrated to our official documentation](https://docs.qiime2.org/2018.2/tutorials/chimera/). 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](http://dx.doi.org/10.1093/bioinformatics/btr381), and the [vsearch](https://github.com/torognes/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](https://docs.qiime2.org/2017.11/tutorials/atacama-soils/).
>
> Download the following files:
>
> - [table.qza](https://view.qiime2.org/?src=https%3A%2F%2Fdocs.qiime2.org%2F2017.11%2Fdata%2Ftutorials%2Fatacama-soils%2Ftable.qza)
> - [rep-seqs.qza](https://view.qiime2.org/?src=https%3A%2F%2Fdocs.qiime2.org%2F2017.11%2Fdata%2Ftutorials%2Fatacama-soils%2Frep-seqs.qza)
>
> # Run _de novo_ chimera checking
>
> ```bash
> 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
>
> ```bash
> 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"
>
> ```bash
> 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
>
> ```
>
> ```bash
> 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
>
> ```
>
> ```bash
> 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"
>
> ```bash
> 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
>
> ```
>
> ```bash
> 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
>
> ```
>
> ```bash
> qiime feature-table summarize --i-table uchime-dn-out/table-nonchimeric.qza --o-visualization uchime-dn-out/table-nonchimeric.qzv
>
> ```
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [February 15, 2018, 6:51pm UTC](https://forum.qiime2.org/t/identifying-and-filtering-chimeric-feature-sequences-with-vsearch/2252/3 "2018-02-15T18:51:26Z")