Quality summary statistics

Commands in mothur
1

Hi,

Is there a tool that summarizes the quality scores at each column in either fastq or qual file? I used to do this by pasting data in excel but my recent datasets are too large for excel to handle this. If this is not a part of Mothur, could you please guide me to an appropriate tool that can help me with this.

Thanks very much,
Ameet

2

This is a good idea and we’ll put it on the list of things to add to mothur in the future - summary.qual. Note that these data are available in seq.error, but that command requires you to have a lot of other information beyond the quality score file.