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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.



fastq_eestats command

See also
FASTQ files
  Expected errors

The fastq_eestats command reports statistics on quality scores and expected errors.

See fastq_eestats2 for a related command which generates a more readable summary.

The report is written to a tabbed text file specifed by the -output option. The distribution Phred (quality) scores and expected errors is reported in terms of the mean and quartiles.

Fields in the tabbed text file are:

Pos: zero-based position in the read.
Reads: number of reads that include this position.
PctRecs: fraction of reads that include this position, as a percentage.
Min_Q: Minimum Q score.
Low_Q: Lower quartile Q score.
Med_Q: Median Q score.
Mean_Q: Mean Q score.
Hi_Q: Upper quartile Q score.
Max_Q: Maximum Q score.
Min_EE: Minimum EEs.
Low_EE: Lower quartile EEs.
Med_EE: Median EEs.
Mean_EE: Mean EEs.
Hi_EE: Upper quartile EEs.
Max_EE: Maximum EEs.

Here, EEs means the total expected errors for positions zero through the current position. The tabbed text file can be loaded into a spreadsheet or other program for generating plots of read quality as in the example below where light green=below lower quartile, dark green=lower quartile, black line=median, red=upper quartile, yellow=above upper quartile.


usearch -fastq_eestats reads.fastq -output eestats.txt