New algorithms
SINTAX taxonomy prediction, paper:
UNOISE2
error-correction (denoising), paper
UCHIME2 chimera detection, paper
UNCROSS
detection and filtering of cross-talk.
Roughly 2% of Illumina reads are assigned to the wrong sample, see
UNCROSS paper.
New commands
alpha_div Calculate
alpha diversity metrics.
annot
Annotate sequences from marker gene experiment (mock or real).
beta_div Calculate
beta diversity metrics.
calc_distmx_smallmem
Reduced-memory version of calc_distmx.
fastx_demux Demultiplex reads by
matching index reads to barcodes.
fastx_info Summarize contents of FASTA/Q file.
fastx_learn Estimate error rates of amplicon reads.
fastx_uniques Find unique
sequences and abundance (new name for derep_fulllength).
filter_phix Filter reads for PhiX.
makeudb_sintax Make indexed
database for sintax.
orient Re-orient nt sequences to same strand
as a reference database (useful for mixed-strand reads).
otutab_norm Normalize OTU table to
same number of reads per sample.
otutab_counts2freqs Convert
OTU table from counts to frequencies.
otutab_freqs2counts Convert
OTU table from frequencies to counts.
otutab_trim Trim low-abundance
counts, OTUs and samples from an OTU table.
otutab_otu_subset Extract a
subset of OTUs from an OTU table.
otutab_sample_subset Extract a subset of samples from an OTU
table.
otutab_stats Report summary
statistics for an OTU table.
search_phix Search for PhiX.
sintax Taxonomy prediction by
SINTAX
algorithm.
uchime2_denovo
Find chimeras in denoised amplicon sequences.
uchime2_ref Find chimeras by
UCHIME2 algorithm using reference database.
uncross Detect and filter cross-talk in
a OTU table.
unoise2
Denoising (error correction) of amplicon reads.