Home Software Services About Contact     
Follow on twitter

Robert C. Edgar on twitter

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.



FASTA files

See also
  Sequence labels
  Annotations in sequence labels

The FASTA sequence file format is widely supported by bioinformatics tools. For a detailed description, see this Wikipedia entry about FASTA.

USEARCH allows lines of any length in a FASTA file. (Some programs limit lines to e.g. 80 characters).

USEARCH does not support comments in FASTA files.

White space characters (blanks and tabs) are discarded if found in sequence data, but many other tools do not allow this and the practice is not recommended.

If the -trunclabels option is given, USEARCH will truncate sequence labels at the first white space (similar to BLAST), otherwise the full label is retained..