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biofilm_030322_qiime2
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conda activate qiime2-2021.4
biom convert -i all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_table.txt -o all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_table.biom --table-type="OTU table" --to-hdf5
qiime tools import \
--input-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_table.biom \
--type 'FeatureTable[Frequency]' \
--input-format BIOMV210Format \
--output-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_table.qza
qiime feature-table summarize \
--i-table all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_table.qza \
--o-visualization all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_table.qzv \
--verbose
qiime feature-table summarize \
--i-table all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_table.qza \
--o-visualization all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_summary.qzv \
--verbose
qiime tools export \
--input-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_summary.qzv \
--output-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_dada2_summary
qiime tools import --input-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set.fasta --output-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set.qza --type 'FeatureData[Sequence]'
qiime feature-table tabulate-seqs --i-data all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set.qza --o-visualization all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_viz.qzv
qiime tools export --input-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_viz.qzv --output-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_viz_export
qiime alignment mafft --i-sequences all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set.qza --p-n-threads 'auto' --o-alignment all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_aligned.qza --verbose
Strategy:
FFT-NS-2 (Fast but rough)
Progressive method (guide trees were built 2 times.)
If unsure which option to use, try 'mafft --auto input output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.
qiime phylogeny fasttree --i-alignment all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_aligned.qza --p-n-threads 'auto' --o-tree all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_aligned_fasttree.qza --verbose
qiime feature-classifier classify-sklearn --i-reads all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set.qza --i-classifier silva-138-99-nb-classifier_extracted_classifier.qza --p-reads-per-batch 10000 --p-n-jobs 4 --o-classification all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_silva_tax.qza --verbose
qiime tools export --input-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_silva_tax.qza --output-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_silva_tax
qiime tools export --input-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_aligned_fasttree.qza --output-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_aligned_fasttree.nwk
qiime tools export --input-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_aligned.qza --output-path all_biofilm_16S_V4V5_030322_pairedend_demux_trimmed_rep_set_aligned.fasta