Package index • Rsearch

All functions

fastx_combine_files(): Combine FASTA/FASTQ files in a directory into a single file or object

fastx_synchronize(): Synchronize FASTA and FASTQ files or objects

make_sintax_db(): Make Sintax database

phyloseq2rsearch(): Convert phyloseq object to Rsearch object

plot_base_quality(): Plot quality scores per position for FASTQ reads

plot_ee_rate_dist(): Plot distribution of expected error (EE) rate of reads

plot_read_quality(): Plot read length vs. read quality

plot_size_dist(): Plot distribution of size values

rsearch2phyloseq(): Convert Rsearch object to phyloseq object

rsearch_obj(): Create Rsearch object

set_vsearch_executable(): Set the VSEARCH executable

taxonomy_tree(): Make a taxonomy tree

vs_alignment_classification(): Taxonomic classification with LCA

vs_cluster_size(): Cluster FASTA sequences

vs_cluster_subseq(): Cluster FASTA sequences

vs_cluster_unoise(): Denoising FASTA sequences

vs_fastq_join(): Join paired-end sequence reads

vs_fastq_mergepairs(): Merge paired-end sequence reads

vs_fastx_subsample(): Subsample sequences

vs_fastx_trim_filt(): Trim and/or filter sequences in FASTA/FASTQ format

vs_fastx_uniques(): Dereplicate sequences

vs_merging_lengths(): Length statistics after merging

vs_optimize_truncee_rate(): Optimize read truncation with truncee_rate

vs_optimize_truncqual(): Optimize read truncation with truncqual

vs_search_exact(): Search for exact full-length matches

vs_sintax(): Taxonomic classification using the Sintax algorithm

vs_uchime_denovo(): Detect chimeras without external references (i.e. de novo)

vs_uchime_ref(): Detect chimeras by comparing sequences to a reference database

vs_usearch_global(): Global pairwise alignment

vsearch(): Test if VSEARCH can be executed