fastx2qiime 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.



fastx2qiime command

Converts a FASTA or FASTQ file with usearch-compatible sample identifiers to QIIME-compatible format.

QIIME embeds sample identifiers into sequence labels using the following rules:
  A label starts with the sample name followed by an underscore (_) and a read number 1, 2, 3 etc.
  The read number is optionally followed by white space and other information which is usually (always?) ignored by the QIIME scripts.
  Only alphanumeric and perdiod (.) characters are allowed in sample names.

The fastx2qiime command converts to QIIME format by finding the sample identifier and appending an underscore and a sequence number. All other information in the label is discarded. Any character in the sample identifier which is not alphameric or a period is replaced by a period.

Input can be in FASTA or FASTQ format. The output filename is specified by -fastqout (FASTQ format) and / or -fastaout (FASTA format). You cannot create FASTQ output from FASTA input.


usearch -fastx2qiime reads.fastq -fastaout reads_qiime.fa