quality scores and the use of pandaseq to join paired-end Illumina reads in QIIME?

74 views
Skip to first unread message

Seaver Wang

unread,
Oct 17, 2016, 3:10:00 PM10/17/16
to Qiime 1 Forum
Hi all,

I've been trying to use pandaseq in conjunction with QIIME to assemble paired-end Illumina reads prior to performing quality filtering and demultiplexing.

What I'm essentially trying to do is use pandaseq in place of join_paired_ends.py as my assembly method (in order to retain more reads), then move on to demultiplexing using split_libraries. I've been having some trouble with this, namely with figuring out how to make my pandaseq output usable with QIIME. 

From what I can understand, pandaseq changes the meaning of the quality scores and therefore the output can't be used to perform quality filtering post-assembly.

As of now, I'm a little confused about how to design my workflow to work with pandaseq. I should join my reads prior to using split_libraries or split_libraries_fastq for quality filtering and demultiplexing, yet if I join my reads using pandaseq, the quality scores are no longer usable for quality filtering. Am I interpreting this correctly? Is there potentially another approach to what I'm trying to do?

I am quite new to QIIME, so please forgive me if I'm missing something obvious!

Best,
Seaver

Colin Brislawn

unread,
Oct 17, 2016, 3:32:21 PM10/17/16
to Qiime 1 Forum
Hello Seaver,

Thanks for getting in touch with us. There are multiple reasonable ways of performing each step in the qiime pipeline. While I can't comment well on pandaseq (never used it), I've got an approach to suggest.

"Is there potentially another approach to what I'm trying to do?"
How about this: 
Join your reads with pandaseq.
Quality filter your reads with pandaseq. 
Use the qiime script add_qiime_labels.py to make a final seqs.fna file.  http://qiime.org/scripts/add_qiime_labels.html

In this method, you will state in the methods section that you use pandaseq for all preprocessing and quality filtering, then proceeded to OTU picking with qiime. I do something similar with the quality filtering tools of vsearch, and it's totally acceptable. 

Let me know if this method will work well for you,
Colin

Seaver Wang

unread,
Oct 18, 2016, 2:53:00 PM10/18/16
to Qiime 1 Forum
Thanks for your answer Colin! I'm attempting this in conjunction with another potential solution at the moment, and I'll hopefully update shortly on how well this worked!
Reply all
Reply to author
Forward
0 new messages