See also
What's new in version 9.1
New algorithms
UNOISE
error-correction (denoising) paper:
SINTAX taxonomy prediction paper:
UCHIME2 chimera detection paper:
New 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.