Always love your mothur!
Would it be relatively easy to add a feature to summary.seqs that allows a fastq input file? I’d love to use that command with a fastq file to get an idea of the range of quality scores directly in the logfile. Something simple like the low and high quality score would be great, but maybe something more complex like a summary of the average quality scores… or the average length at which QS remains above a certain threshold…
Maybe something like this(hypothetical numbers) where QS shows the range of QS over individual reads, aveQS shows the range of average QS, and LenQS shows the range of read lengths at which the base quality score remains above a certain threshold.
[img]Start End NBases Ambigs Polymer NumSeqs QS aveQS LenQS
Minimum: 1 35 35 0 2 1 0 1
2.5%-tile: 1 147 147 0 4 59794 3 100
25%-tile: 1 151 151 0 4 597933 25 130
Median: 1 168 168 0 4 1195866 30 130
75%-tile: 1 190 190 0 5 1793798 30 140
97.5%-tile: 1 193 193 14 6 2331937 35 160
Maximum: 1 303 302 199 151 2391730 40 190
Mean: 1 169.435 169.435 1.44417 4.4614 30.275 130.475
of Seqs: 2391730[/img]
Thoughts? Thanks!