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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_getseq command

See also


Extract one or more sequences from a FASTA or FASTQ file. The label is given by the -label option. Only one -label option may be specified.

If the -label_substr_match option is specified, then the label given on the command-line may be a substring of a sequence label, which may result in more than one sequence being extracted.

Output is written to -fastaout (FASTA) and/or -fastqout (FASTQ). You cannot use -fastqout if the input is FASTA because the quality scores are not known.


usearch -fastx_getseq reads.fa -label FO09O1002IH8ZO -fastqout the_read.fq -fastaout the_read.fa

usearch -fastx_getseq genome.fa -label chromosome_3 -fastaout chr3.fa