Man pages for demulticoder
Simultaneous Analysis of Multiplexed Metabarcodes
| assign_tax | Assign taxonomy functions |
| assignTax_as_char | Combine taxonomic assignments and bootstrap values for each... |
| assign_taxonomyDada2 | Assign taxonomy |
| convert_asv_matrix_to_objs | Filter ASV abundance matrix and convert to 'taxmap' and... |
| countOverlap | Count overlap to see how well the reads were merged |
| createASVSequenceTable | Make ASV sequence matrix |
| cut_trim | Main command to trim primers using 'Cutadapt' and core... |
| filter_and_trim | Wrapper function for 'filterAndTrim' function from 'DADA2',... |
| format_abund_matrix | Format ASV abundance matrix |
| format_database | General functions to format user-specified databases |
| format_db_16S | An 16S database that has modified headers and is output in... |
| format_db_its | An ITS database that has modified headers and is output in... |
| format_db_other1 | An other, user-specified database that is initially in the... |
| format_db_other2 | An second user-specified database that is initially in the... |
| format_db_rps10 | Create modified reference rps10 database for downstream... |
| get_fastq_paths | Retrieve the paths of the filtered and trimmed Fastq files |
| get_post_trim_hits | Get primer counts for reach sample after primer removal and... |
| get_pre_primer_hits | Get primer counts for reach sample before primer removal and... |
| get_read_counts | Final inventory of read counts after each step from input to... |
| infer_asv_command | Function to infer ASVs, for multiple loci |
| infer_asvs | Core 'DADA2' function to learn errors and infer ASVs |
| make_abund_matrix | Quality filtering to remove chimeras and short sequences |
| make_asv_abund_matrix | Make an amplified sequence variant (ASV) abundance matrix for... |
| make_cutadapt_tibble | Prepare for primmer trimming with 'Cutadapt'. Make new... |
| make_seqhist | Plots a histogram of read length counts of all sequences... |
| merge_reads_command | Merge forward and reverse reads |
| orient_primers | Take in user's forward and reverse sequences and creates the... |
| plot_post_trim_qc | Wrapper script for plotQualityProfile after trim steps and... |
| plot_qc | Wrapper function for plotQualityProfile function |
| prep_abund_matrix | Prepare final ASV abundance matrix |
| prepare_metadata_table | Read metadata file from user and combine and reformat it,... |
| prepare_reads | Prepare reads for primer trimming using 'Cutadapt' |
| primer_check | Matching Order Primer Check |
| process_single_barcode | Run 'DADA2' taxonomy functions for single metabarcode |
| read_fastq | Takes in the FASTQ files from the user and creates a... |
| read_parameters_table | Take in user's 'DADA2' parameters and make a data frame for... |
| read_prefilt_fastq | A function for calling read_fastq, primer_check, and... |
| remove_ns | Wrapper function for core 'DADA2' filter and trim function... |
| run_cutadapt | Core function for running 'Cutadapt' |
| setup_directories | Set up directory paths for subsequent analyses |
