Package index
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assign_taxonomy_sintax() - Run taxonomy assignment (SINTAX algorithm)
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check_system_requirements() - Check external software requirements and report missing programs
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compare_seqs() - Compare different sequences per taxon
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create_excel_report() - Create an Excel report
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dada2_denoise() - Run DADA2 denoising
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dada_learn_errors() - Learn error rates
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do_combine_alignments() - Combine all BAM alignment files into a single one
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do_demux() - Group sequences by sample index combination
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do_infer_all_barcodes() - Infer barcode sequences for all samples
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do_primer_search() - Search and remove primer sequences
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do_assign_compare_taxonomy()do_assign_taxonomy()do_compare_taxonomy() - Run the taxonomy assignment and compare with provided taxonomic names of specimens
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do_trim_demux() - Search and remove primers and sample indexes
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fix_homopolymers() - Attempt at "fixing" the consensus sequence in a homopolymer region
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get_gbif_taxa() - Match taxonomic names/lineages against the GBIF taxonomy
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infer_barcode() - Infer barcode sequence(s) from raw reads in a single sample
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init_pipeline() - Scaffold the targets Pipeline
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load_taxdb() - Download a taxonomic database and save it in UTAX format
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parse_primer_tab() - Parse a data frame with primer information
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parse_sample_tab() - Parse a data frame with sample metadata
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read_xlsx_primer_tab() - Read primer information from Excel file
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read_xlsx_sample_tab() - Read sample metadata from Excel file
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set_global_opts() - Set global options
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try_split_haplotypes() - Attempts splitting sequence cluster into two haplotypes.