Newbie to MiSeq, QIIME workflow question

[rc630]

Hi all,

I just got my MiSeq data for fungal ITS sequences in a large number of samples. I am going to be using QIIME to do the analysis and I have a basic workflow from another person, but I wasn't sure about where paired end assembly would be in the workflow.

I know that MiSeq data is already demultiplexed and that I will be using the split_libraries_fastq.py function, but do I need to do paired end assembly before that? What program is best to use for that, PANDASeq or join_paired_ends.py? For each sample I have two FASTQ files, Read 1 and Read 2, but the workflow I have does not address that.

Thanks

[thermophile]

Here's my processing script for getting already demultiplexed sequences to the point of running through qiime. The for loop makes sense for the way that I name my samples/sequences, but may not make sense for your naming convention.

https://github.com/krmaas/bioinformatics/blob/master/qiime.process.txt

[Brian Bushnell]

I know that MiSeq data is already demultiplexed and that I will be using the split_libraries_fastq.py function, but do I need to do paired end assembly before that? What program is best to use for that, PANDASeq or join_paired_ends.py?

Yes, you should merge the paired reads into single reads. The best program for that purpose is BBMerge.