ess-dive_amplicon_bioinformatic_metadata_template_2021-10-03.csv

Columns,read_pair_method,barcode_error_rate,read_length_cutoff,quality_filter_cutoff,chimera_method,denoise_method,sequence_error_cutoff,clustering_method,clustering_cutoff,sequence_filtering,abundance_filtering,
Contains,"Method (platform, software, commands) uses to pair forward and reverse reads if applicable.",Maximum error rate in the barcodes used to match reads with samples during dereplication. Number of mismatched bases divided by the length of the matching barcode.,Read length in base pairs below which the read is excluded from sequence-by-sample table.,The minimum PHRED quality score accepted for base calls in the reads.,"Method (platform, software, commands) used to detect and remove chimeric sequences formed during PCR amplification.","Method (platform, software, commands) used to reconstruct true sequence variants and recover their frequencies from reads with sequencing errors.",Per nucleotide or per read error estimate used as input for a denoising method.,"Method (platform, software, commands) used to collapse similar sequences into single operational taxonomic units.
",Percent sequence similarity threshold used to cluster sequences into operational taxonomic units.,Define a filter used to include or exclude sequences based on their similarity to a reference database or known contaminant list.,Define a filter used to include or exclude sequences based on their prevalence or abundance in samples.,
Formatting,"Text; If not using paired reads, enter ""N/A"".",Proportion between 0 and 1,Integer,Integer,"If not performed, enter ""N/A"".","Text; If not performed, enter ""N/A"".","Text; If not performed, enter ""N/A"".","Text; If not performed, enter ""N/A"".","Integer; If not performed, enter ""N/A"".","Text; If not performed, enter ""N/A"".","Text; If not performed, enter ""N/A"".",
Requirement,Required,Required,Required,Required,Required,Required if a denoising method is used.,Required if a denoising method is used.,Required if a clustering method is used.,Required if a clustering method is used.,Required if a positive or negative sequence filter was used.,Required if a filter for sequence count was used.,
Example,"Qiime2 dada2 denoise-paired, --p-min-overlap 20",0.1,150,30,Qiime2 dada2 denoise-paired --p-chimera-method 'consensus' --p-min-fold-parent-over-abundance 1.0,"Qiime2 dada2 denoise-paired --p-pooling-method 'independent', --p-n-reads-learn 1000000",Qiime 2 dada2 --p-max-ee-f  2 --p-max-ee-r 2,"Qiime 2 vsearch cluster-features-open-reference, SILVA 138 SSU",97,Excluded reads matching PhiX at 90% sequence identity.,Excluded sequences with fewer than 10000 reads total in the dataset.