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QIIME2_Processing.sh
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qiime tools import \
--type "SampleData[PairedEndSequencesWithQuality]" \
--input-format PairedEndFastqManifestPhred33V2 \
--input-path /mnt/datasets/project_2/nasa/nasa_dust_manifest.tsv \
--output-path demux_seqs.qza
qiime demux summarize \
--i-data demux_seqs.qza \
--o-visualization demux_seqs.qzv
qiime dada2 denoise-paired \
--i-demultiplexed-seqs /data/nasa_data/data_process/demux_seqs.qza \
--p-trim-left-f 0 \
--p-trim-left-r 0 \
--p-trunc-len-f 262 \
--p-trunc-len-r 233 \
--o-representative-sequences /data/nasa_data/data_process/rep-seqs.qza \
--o-table /data/nasa_data/data_process/table.qza \
--o-denoising-stats /data/nasa_data/data_process/stats.qza
qiime metadata tabulate \
--m-input-file stats.qza \
--o-visualization stats.qzv
qiime feature-table filter-samples \
--i-table table.qza \
--m-metadata-file /data/nasa_data/data_process/updated_nasa_dust_metadata.tsv \
--o-filtered-table filtered_table.qza
qiime feature-table summarize \
--i-table filtered_table.qza \
--o-visualization table.qzv \
--m-sample-metadata-file /data/nasa_data/data_process/updated_nasa_dust_metadata.tsv
qiime feature-table tabulate-seqs \
--i-data rep-seqs.qza \
--o-visualization rep-seqs.qzv
qiime feature-classifier extract-reads \
--i-sequences /mnt/datasets/silva_ref_files/silva-138-99-seqs.qza \
--p-f-primer GTGCCAGCMGCCGCGGTAA \
--p-r-primer GGACTACHVGGGTWTCTAAT \
--p-trunc-len 233 \
--o-reads ref-seqs-trimmed.qza
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads ref-seqs-trimmed.qza \
--i-reference-taxonomy /mnt/datasets/silva_ref_files/silva-138-99-tax.qza \
--o-classifier classifier.qza
qiime feature-classifier classify-sklearn \
--i-classifier classifier.qza \
--i-reads /data/nasa_data/data_process/rep-seqs.qza \
--o-classification taxonomy.qza
qiime taxa filter-table \
--i-table filtered_table.qza \
--i-taxonomy taxonomy.qza \
--p-exclude mitochondria,chloroplast \
--o-filtered-table table-no-mitochondria-no-chloroplast.qza
qiime feature-table summarize \
--i-table table-no-mitochondria-no-chloroplast.qza \
--o-visualization dust_table-no-mitochondria-no-chloroplast.qzv \
--m-sample-metadata-file /data/nasa_data/data_process/updated_nasa_dust_metadata.tsv
qiime phylogeny align-to-tree-mafft-fasttree \
--i-sequences rep-seqs.qza \
--o-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza \
--o-tree unrooted-tree.qza \
--o-rooted-tree rooted-tree.qza
qiime tools export \
--input-path taxonomy.qza \
--output-path /data/nasa_data/data_process/nasa_export/taxonomy_export
qiime tools export \
--input-path rooted-tree.qza \
--output-path /data/nasa_data/data_process/nasa_export/rooted_tree_export
qiime tools export \
--input-path table.qza \
--output-path /data/nasa_data/data_process/nasa_export/table_export
biom convert \
-i feature-table.biom \
--to-tsv \
-o feature-table.txt