4.20. amplicon16S_analysis¶
Running 16S amplicon (from BAM format) sequencing analysis with qiime.
4.20.1. Inputs¶
4.20.1.1. Required inputs¶
amplicon16S_analysis.keep_untrimmed_reads
Boolean — Default: None
???
amplicon16S_analysis.reads_bam
Array[File] — Default: None
???
amplicon16S_analysis.trained_classifier
File — Default: None
???
4.20.1.2. Advanced inputs¶
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amplicon16S_analysis.deblur.trim_length_var
Int — Default: 300
Length that all seqeuences will be trimmed, and discard any sequences that are not at least this long.
amplicon16S_analysis.trim_reads.forward_adapter
String — Default: "CTGCTGCCTCCCGTAGGAGT"
Forward amplicon primer sequence.
4.20.1.3. Other inputs¶
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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.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.memory_mb
Int — Default: 2000
???
amplicon16S_analysis.trim_reads.min_length
Int — Default: 1
Minimum length of the read, cutadapt will discard anything that is shorter than n bp AFTER trimming.Set to default.
amplicon16S_analysis.trim_reads.reverse_adapter
String — Default: "AGAGTTTGATCCTGGCTCAG"
Reverse amplicon primer sequence.
4.20.2. Outputs¶
amplicon16S_analysis.deblur.feature_table
File
A table that represent the number of of features per sample, the number of samples a given feature is found in.
amplicon16S_analysis.deblur.representative_seqs_qza
File
Generate a list of the representative sequences. May be useful to the user if they want to blast these sequences or check for correct trimming.
amplicon16S_analysis.deblur.representative_table_qza
File
Generate a table of the representaitve sequences.
amplicon16S_analysis.deblur.visualize_stats
File
Generate visualization of deblur stats.
amplicon16S_analysis.join_paired_ends.joined_end_reads_qza
File
Merge paired read file.
amplicon16S_analysis.join_paired_ends.joined_end_visualization
File
This summary is especially useful for assessing the length of linked reads and the quality scores at each sequence base position.
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
File contains all samples names.
amplicon16S_analysis.tax_analysis.rep_seq_list
File
Generate list of representative sequences.
amplicon16S_analysis.tax_analysis.tax_classification_graph
File
Create a bar graph of your taxonomic classification.
amplicon16S_analysis.trim_reads.trimmed_reads_qza
File
Trimmed reads data file.
amplicon16S_analysis.trim_reads.trimmed_visualization
File
A diagram that compares your demuxed reads before and after cutting (i.e. length of reads, how many reads were retained).
Generated using WDL AID (1.0.0)