Join paired end reads

Having high quality, longer reads helps with taxonomy assignment and classification. Thus, if your forward and reverse reads overlap you should join them. Note that this is not currently possible automatically in Qiita but we will be adding this functionality in the future.

Note

Please note that most of these guides assume you have a working QIIME installation and basic knowledge on the usage of the command line.

Joining forward and reverse reads for raw files

You could use join_paired_ends.py and then upload your joined sequence and barcode files for processing. Then you will upload the resulting joined file to Qiita.

Joining forward and reverse reads for per sample FASTQ files without barcodes and primers

You could use multiple_join_paired_ends.py and then upload your joined sequence and barcode files for processing. Then you will upload the resulting joined per sample files to Qiita.

Per sample FASTQ files without barcodes but with primer information with overlapping regions

To process this kind of files you will need to run two steps:

1. Run multiple_join_paired_ends.py to stitch the reads. See multiple_join_paired_ends.py.

2. Run multiple_extract_barcodes.py to strip out the primers. You will need to use a parameter file with:

   extract_barcodes:input_type barcode_paired_stitched
   extract_barcodes:bc1_len X
   extract_barcodes:bc2_len Y
   

Be sure to replace X and Y for your actual values.

These steps will generate a folder per sample, each with 2 files: the reads and the barcodes. You will need to upload just the reads and ignore the generated barcode files.