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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

nastout option

Output file for search hits in NAST format.

If -nastout is specified, then the search database must be a multiple alignment in FASTA format.

Hits are written to the -nastout file as follows. Only the query sequence is written; if you need to know the target sequence or label, you can use one of the other standard output files and match up the query labels. Gaps are added as needed to align to that target sequence. Insertions relative to that target are deleted, so that the resulting sequence has exactly the same number of columns as the database multiple alignment. The deleted insertions are noted by appending an "ins=" annotation to the label, as in the following example:

>Read_XXYZQVA23;ins=AGCGTGAG/2154,TT/3972,G/4029,CCATTCCACGG/4401;

The ins= annotation is a comma-separated list of insertions. Each insertion gives the deleted sequence and column number in the multiple alignment. So, for example, TT/3972 means that two TTs were deleted following the letter in the query sequence that appears in column 3972 in the multiple alignment.

Gap characters can be specified by -nast_delgap, -nast_locgap, -nast_padgap and -nast_termgap. Default is dash (-) except for terminal gaps, which default to dot (.).

Example

-usearch_global reads.fastq -db gg_13_5_ssualign.fasta -strand both -id 0.95 \
  -blast6out hits.b6 -nastout reads.nast