Processing and Analyzing Amplicon Sequence Data

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Documentation for package ‘Rsearch’ version 1.0.0

• DESCRIPTION file.

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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_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