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!