Does demultiplex step trim reads?

Skip to first unread message

Sanjeev Sariya

Sep 1, 2016, 4:49:02 PM9/1/16
to Qiime 1 Forum
Hi QIIME developers,

I'm working on Illumina paired end 300bp reads. I join the reads with ea-utils.
Post demultiplexing stats for read length looks like:

Median length: 438
Min length: 318
Max length: 538
Mean length 438

Command used:


R2=R2R3.paired.fq -i $R1 -o ./demultiplex -b $R2 -m ./mapping_qiime.txt --max_barcode_errors 1 --sequence_max_n 0 --phred_quality_threshold 20 --max_bad_run_length 300 --min_per_read_length_fraction 0.75 --barcode_type 16

I'm providing .75 as the percent for min. per read length for consecutive high quality case calls. 


1- At what point QIIME trimmed read to 318?

2- By what metric is QIIME trimming reads?

Kindly help me to understand this.

Thanks in advance.


Jose Antonio Navas Molina

Sep 2, 2016, 11:25:58 AM9/2/16
to Qiime 1 Forum
Hi Sanjeev,

Qiime uses a sliding window to check the quality of the reads. Multiple steps are performed during the quality control of the sequences. Since I don't wanna do a bad summary of the algorithm, I think the safest is to point you to the actual article that describes the algorithm:

Figure 1 is a good summary on how the quality control works in Qiime.

Reply all
Reply to author
0 new messages