Using barcoded templates

Sequencing experiments that involve sample amplification often lose the information on how many different genomes/templates were actually sequenced. Attaching unique barcodes to the input templates before their amplification allows recovering the counts on the number of amplified templates. AccuNGS allows for long amplicons and does not assume anything about the length of the amplified region. Furthermore, the usage of Nextera XT to insert sequencing indexes and adapters at random positions results with the barcode in different positions for different reads (if present at all). To address this we’ve written a python utility that performs an alignment of each read against an RT/PCR primer containing a degenerate region that allows tagging reads with their corresponding barcode (if present). The code is available as a python package here.