4.4. amplicon16S_analysis¶

Running 16S amplicon (from BAM format) sequencing analysis with qiime.

4.4.1. Inputs¶

amplicon16S_analysis.keep_untrimmed_reads
Boolean — Default: None
???

amplicon16S_analysis.reads_bam
Array[File] — Default: None
???

amplicon16S_analysis.trained_classifier
File — Default: None
???

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amplicon16S_analysis.deblur.cpu
Int — Default: 1
???

amplicon16S_analysis.deblur.disk_size_gb
Int — Default: ceil((2 * size(joined_end_reads_qza,"GiB"))) + 5
???

amplicon16S_analysis.deblur.docker
String — Default: "quay.io/broadinstitute/qiime2"
???

amplicon16S_analysis.deblur.memory_mb
Int — Default: 2000
???

amplicon16S_analysis.deblur.trim_length_var
Int — Default: 300
???

amplicon16S_analysis.join_paired_ends.cpu
Int — Default: 1
???

amplicon16S_analysis.join_paired_ends.disk_size_gb
Int — Default: ceil((2 * size(trimmed_reads_qza,"GiB"))) + 50
???

amplicon16S_analysis.join_paired_ends.docker
String — Default: "quay.io/broadinstitute/qiime2"
???

amplicon16S_analysis.join_paired_ends.memory_mb
Int — Default: 2000
???

amplicon16S_analysis.qiime_import_from_bam.cpu
Int — Default: 5
???

amplicon16S_analysis.qiime_import_from_bam.disk_size_gb
Int — Default: ceil((2 * 20)) + 5
???

amplicon16S_analysis.qiime_import_from_bam.docker
String — Default: "quay.io/broadinstitute/qiime2"
???

amplicon16S_analysis.qiime_import_from_bam.memory_mb
Int — Default: 7000
???

amplicon16S_analysis.tax_analysis.cpu
Int — Default: 1
???

amplicon16S_analysis.tax_analysis.disk_size_gb
Int — Default: 375
???

amplicon16S_analysis.tax_analysis.docker
String — Default: "quay.io/broadinstitute/qiime2"
???

amplicon16S_analysis.tax_analysis.memory_mb
Int — Default: 5
???

amplicon16S_analysis.trim_reads.cpu
Int — Default: 4
???

amplicon16S_analysis.trim_reads.disk_size_gb
Int — Default: ceil((2 * size(reads_qza,"GiB"))) + 5
???

amplicon16S_analysis.trim_reads.docker
String — Default: "quay.io/broadinstitute/qiime2"
???

amplicon16S_analysis.trim_reads.forward_adapter
String — Default: "CTGCTGCCTCCCGTAGGAGT"
???

amplicon16S_analysis.trim_reads.memory_mb
Int — Default: 2000
???

amplicon16S_analysis.trim_reads.min_length
Int — Default: 1
???

amplicon16S_analysis.trim_reads.reverse_adapter
String — Default: "AGAGTTTGATCCTGGCTCAG"
???

amplicon16S_analysis.deblur.feature_table
File
???

amplicon16S_analysis.deblur.representative_seqs_qza
File
???

amplicon16S_analysis.deblur.representative_table_qza
File
???

amplicon16S_analysis.deblur.visualize_stats
File
???

amplicon16S_analysis.join_paired_ends.joined_end_reads_qza
File
???

amplicon16S_analysis.join_paired_ends.joined_end_visualization
File
???

amplicon16S_analysis.qiime_import_from_bam.reads_qza
File
All unaligned reads in a single QZA (QIIME) file

amplicon16S_analysis.qiime_import_from_bam.samplename_master_sheet
String
???

amplicon16S_analysis.tax_analysis.rep_seq_list
File
???

amplicon16S_analysis.tax_analysis.tax_classification_graph
File
???

amplicon16S_analysis.trim_reads.trimmed_reads_qza
File
???

amplicon16S_analysis.trim_reads.trimmed_visualization
File
???

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