9.2 features
Calculate alpha and beta diversity
metrics.
New OTU table commands.
9.2 commands
alpha_div Calculate
alpha diversity metrics
beta_div Calculate
beta diversity metrics, clusters and trees
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
otutab_sample_subset Extract a subset of samples
otutab_stats Report summary
statistics for an OTU table
9.1 algorithm
UNCROSS
detection and filtering of cross-talk.
Roughly 2% of reads
are assigned to the wrong sample.
The UNCROSS algorithm can detect
and filter cross-talk.
See
UNCROSS paper for
details.
9.1 commands
uncross Detect and filter cross-talk in
a OTU table.
unoise2 Updated
version of unoise using the UNOISE2 algorithm (Edgar
2016).
9.0 algorithms
UNOISE
error-correction (denoising) paper:
SINTAX taxonomy prediction paper:
UCHIME2 chimera detection paper:
9.0 commands
annot
Annotate sequences from marker gene experiment (mock or real).
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 Determine 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).
search_phix Search for PhiX.
sintax Taxonomy prediction by
SINTAX
algorithm.
tree2clusters
Generate clusters from a tree by setting an identity cutoff.
uchime2_denovo
Find chimeras in denoised amplicon sequences.
uchime2_ref Find chimeras by
UCHIME2 algorithm using reference database.
unoise
Denoising (error correction) of amplicon reads.
Backwards compatibility with v8
Version 9 should be mostly backwards compatible
with version 8 as there are relatively few changes to the internal code
compared with previous major version updates. If users run into any
compatibility problems I will update this page with details.
Deprecated
The derep_fulllength command is still supported but is deprecated. Use
fastx_uniques for new scripts.
No longer supported
uchime_denovo -- Does not
work well with Illumina. Use an old version of usearch if you have 454
reads.
uchime_ref -- Replaced by uchime2_ref.