fastx_getlabels command
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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.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



fastx_getlabels command

Writes the sequence labels from a FASTQ or FASTA file to a text file with one label per line. The output file name is given by the -output option.

With FASTA format, the effect is essentially the same as:

grep "^>" input.fa | sed "-es/^>//" > labels.txt

With FASTQ format, there is no simple way to do this using Linux commands because the Q score sequence can start with the same character(s) as a read label.


usearch -fastx_getlabels reads.fq -output labels.txt