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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

userfields field names

The userout option specifies a tabbed text output file with field names specified by the -userfields option.

For example, the following will give the same output as -blast6out hits.txt

 usearch -ublast reads.fastq -db proteins.fa -evalue 0.01 -userout hits.txt
   -userfields query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits
 

 
query   Query sequence label.
target   Target sequenc label.
clusternr   Cluster number.
evalue   E-value.
id   Fractional identity.
mid   Fraction of letter pairs that match.
pctpv   Percent positives (substitution score > 0).
pctgaps   Percent gap columns.
pairs   Number of letter pair columns.
gaps   Number of gapped columns.
qlo   0-based start position of alignment in query sequence.
qhi   0-based end position of alignment in query sequence.
tlo   0-based start position of alignment in target sequence.
thi   0-based end position of alignment in target sequence.
pv   Number of positive columns (substitution score > 0).
ql   Query sequence length.
tl   Target sequence length.
qs   Query segment length.
ts   Target segment length.
alnlen   Number of alignment columns.
opens   Number of gap opens.
exts   Number of gap extensions (does not include gap opens).
raw   Raw alignment score.
bits   Bit score.
aln   Alignment as string M=letter pair, D=delete (gap in query), I=insert (gap in target).
caln   Compressed alignment (see uc file format).
qseq   Full-length query sequence.
tseq   Full-length target sequence.
qstrand   Query strand.
tstrand   Target strand.
qrow   Aligned query segment with gaps.
trow   Aligned target segment with gaps.
qrowdots   Aligned query segment with gaps and dots for matched positions.
trowdots   Aligned target segment with gaps and dots for matched positions.
qframe   Query frame (-3 to +3).
tframe   Target frame (-3 to +3).
mism   Number of mismatches.
ids   Number of columns with matching letters.
qcov   Fraction of query sequence covered by alignment.
tcov   Fraction of target sequence covered by alignment.
diffs   Number of differences (gaps + mismatches).
abskew   Abundance skew.
qlor   0-based query start coordinate.
qhir   0-based query end coordinate.
tlor   0-based target start coordinate.
thir   0-based target end coordinate.
orflo   Start coordinate of query ORF in nt sequence.
orfhi   End coordinate of query ORF in nt sequence.
orfframe   Frame of query ORF.