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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

fastx_getseqs command

See also
 
fastx_getseq

  fastx_getsubseq

Extract sequences from a FASTA or FASTQ file by matching sequence labels.

The -label option specifies a string to match the label.

The -labels option specifies the name of a text file. Each line of the text file contains a string to match the label.

The -label_word option specifies a word which must match the label. The match must be to a whole word.

The -label_words option specifies a text file. Each line of the text file contains a word to match the label.

Matches specified by -label and -labels are case-insensitive.

Matches specified by -label_word and -label_words are case-sensitive.

The -label_field option specifies the name of a name=xxx; style annotation in the label. Word matches by -label_word or -label_words is then performed on the xxx string, not the full label.

The -label_substr_match option specifies that matches to a string given by -label or -labels may be to a substring of the label. Otherwise the strings must be identical.

Sequence with labels that match are written to filenames given by -fastaout (FASTA) and/or -fastqout (FASTQ).

Sequences which do not match are written to filename given by -notmatched (FASTA) or -notmatchedfq (FASTQ).

Example

usearch -fastx_getseqs seqs.fa -labels labels.txt -fastaout subset.fa