See also
What's new in
version 9
What's new in version 8
What's new in version 7
Improved OTU / denoising analysis protocol
Pipeline documentation
OTU quality control
New algorithms
UNBIAS correct
for abundance bias in a OTU table
SEARCH_16S find 16S genes in
contigs and chromosomes
SINAPS
predict attributes (traits) from marker gene sequences
New commands
alpha_div_rare
calculate rarefaction curves for alpha
diversity metrics
closed_ref closed-reference OTU assignment
fasta_explode create separate
file for every sequence in a FASTA file
fasta_stripgaps remove gaps
from FASTA file
fastq_sra_splitpairs recover R1 and R2 reads from concatenated or
interleaved SRA
file
fastx2qiime convert
sample identifiers from usearch to QIIME format
fastx_demux assign reads to samples
(demultiplex) using embedded barcodes or index
reads
fastx_getlabels extract
sequence labels from FASTA or FASTQ file
fastx_get_sample_names
get sample names in read labels, useful for checking correct formatting
fastx_relabel re-label sequences
in FASTA or FASTQ file
fastx_strip_annots remove usearch-style annotations from sequence
labels
fastx_uniques_persample find unique sequences per sample
filter_lowc Filter low-complexity
sequences.
otutab generate OTU table
otutab_group combine (sum) counts
for groups of samples
otutab_merge merge OTU tables by matching OTU and
sample identifiers
otutab_sortotus sort OTU table by decreasing OTU size
otutab_subsample subsample
(rarefy) OTU table to smaller number of reads
qiimemap2otutab convert QIIME
map file to OTU table
search_16s
find 16S genes in contigs and chromosomes
sinaps predict attributes (traits) from
marker gene sequences
sintax_summary taxonomy summary for making figures
etc.
uchime3_denovo
filter chimeras in denoised amplicon sequences
udb2bitvec create bit vector index
for search_16s command
unbias
correct for abundance bias
unoise3 denoise amplicon reads
(improved algorithm)