Reference files for QIIME 2
======

QIIME 2 is a comprehensive microbiome bioinformatics platform.

 - Website: https://qiime2.org/
 - Citation: Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC,
   Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y.
   Reproducible, interactive, scalable and extensible microbiome data
   science using QIIME 2. Nature biotechnology. 2019 Aug;37(8):852-7.

Built using QIIME 2 v2022.8.

Phylogeny:

Use phylogeny/tree.nwk. Command:

```
qiime tools import --type Phylogeny[Rooted] \
  --input-path tree.nwk --output-path phylogeny.qza
```

Taxonomy:

Use taxonomy/lineages.txt, but add 'Feature ID' and 'Taxon' as the header.
Command:

```
qiime tools import --type FeatureData[Taxonomy] \
  --input-path lineages.txt --output-path taxonomy.qza
```

Example usage:

Generate an OGU table from sequence alignments (requires q2-woltka):

 - Website: https://library.qiime2.org/plugins/q2-woltka/42/

```
qiime woltka classify \
  --i-alignment align_sam.qza \
  --p-target-rank none \
  --o-classified-table ogu_table.qza
```

Generate interactive bar plots at individual taxonomic levels:

```
qiime taxa barplot \
  --i-table ogu_table.qza \
  --i-taxonomy taxonomy.qza \
  --m-metadata-file metadata.tsv \
  --o-visualization taxa_plot.qzv
```

Perform community diversity analyses using phylogeny-aware and -free metrics:

```
qiime diversity core-metrics-phylogenetic \
  --i-table ogu_table.qza \
  --i-phylogeny phylogeny.qza \
  --p-sampling-depth 10000 \
  --m-metadata-file metadata.tsv \
  --output-dir .
```