Rsearch1.0.0 package

Combine FASTA/FASTQ files in a directory into a single file or object

Synchronize FASTA and FASTQ files or objects

Make Sintax database

Convert phyloseq object to Rsearch object

Plot quality scores per position for FASTQ reads

Plot distribution of expected error (EE) rate of reads

Plot read length vs. read quality

Plot distribution of size values

Create Rsearch object

Rsearch

Convert Rsearch object to phyloseq object

Set the VSEARCH executable

Make a taxonomy tree

Taxonomic classification with LCA

Cluster FASTA sequences

Cluster FASTA sequences

Denoising FASTA sequences

Join paired-end sequence reads

Merge paired-end sequence reads

Subsample sequences

Trim and/or filter sequences in FASTA/FASTQ format

Dereplicate sequences

Length statistics after merging

Optimize read truncation with truncee_rate

Optimize read truncation with truncqual

Search for exact full-length matches

Taxonomic classification using the Sintax algorithm

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

Detect chimeras by comparing sequences to a reference database

Global pairwise alignment

Test if VSEARCH can be executed