R: Processing and Analyzing Amplicon Sequence Data

# Processing and Analyzing Amplicon Sequence Data

## Documentation for package ‘Rsearch’ version 1.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

alignment_classification | Taxonomic classification with LCA
chimera | Detect chimeras without external references (i.e. de novo)
classify | Taxonomic classification using the Sintax algorithm
cluster | Cluster FASTA sequences
cluster_size | Cluster FASTA sequences
cluster_unoise | Denoising FASTA sequences
denoise | Denoising FASTA sequences
dereplicate | Dereplicate sequences
fasta_combine_files | Combine FASTA/FASTQ files in a directory into a single file or object
fasta_synchronize | Synchronize FASTA and FASTQ files or objects
fastq_combine_files | Combine FASTA/FASTQ files in a directory into a single file or object
fastq_join | Join paired-end sequence reads
fastq_mergepairs | Merge paired-end sequence reads
fastq_synchronize | Synchronize FASTA and FASTQ files or objects
fastx_combine_files | Combine FASTA/FASTQ files in a directory into a single file or object
fastx_subsample | Subsample sequences
fastx_synchronize | Synchronize FASTA and FASTQ files or objects
fastx_trim_filt | Trim and/or filter sequences in FASTA/FASTQ format
fastx_uniques | Dereplicate sequences
global_alignment | Global pairwise alignment
join | Join paired-end sequence reads
lca | Taxonomic classification with LCA
lca_classification | Taxonomic classification with LCA
make_sintax_db | Make Sintax database
mergepairs | Merge paired-end sequence reads
merging_lengths | Length statistics after merging
optimize_truncee_rate | Optimize read truncation with truncee_rate
optimize_truncqual | Optimize read truncation with truncqual
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
search_exact | Search for exact full-length matches
set_vsearch_executable | Set the VSEARCH executable
sintax | Taxonomic classification using the Sintax algorithm
sintax_db | Make Sintax database
subsample | Subsample sequences
taxonomy_distance | Creates a distance object based on taxonomy information.
taxonomy_tree | Make a taxonomy tree
trim_filt | Trim and/or filter sequences in FASTA/FASTQ format
uchime_denovo | Detect chimeras without external references (i.e. de novo)
uchime_ref | Detect chimeras by comparing sequences to a reference database
unoise | Denoising FASTA sequences
usearch_global | Global pairwise alignment
vsearch | Test if 'VSEARCH' can be executed
vs_alignment_classification | Taxonomic classification with LCA
vs_cluster | Cluster FASTA sequences
vs_cluster_length | Cluster FASTA sequences
vs_cluster_size | Cluster FASTA sequences
vs_cluster_subseq | Cluster FASTA sequences
vs_cluster_unoise | Denoising FASTA sequences
vs_fasta_dereplicate | Dereplicate sequences
vs_fasta_join | Join paired-end sequence reads
vs_fasta_mergepairs | Merge paired-end sequence reads
vs_fasta_subsample | Subsample sequences
vs_fasta_trim_filt | Trim and/or filter sequences in FASTA/FASTQ format
vs_fasta_uniques | Dereplicate sequences
vs_fastq_dereplicate | Dereplicate sequences
vs_fastq_join | Join paired-end sequence reads
vs_fastq_mergepairs | Merge paired-end sequence reads
vs_fastq_subsample | Subsample sequences
vs_fastq_trim_filt | Trim and/or filter sequences in FASTA/FASTQ format
vs_fastq_uniques | Dereplicate sequences
vs_fastx_dereplicate | Dereplicate sequences
vs_fastx_join | Join paired-end sequence reads
vs_fastx_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_mergepairs | Merge paired-end sequence reads
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_subsample | Subsample sequences
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