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Updated: Sep 23, 2025
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment
Chiann-Ling C Yeh1, Clara J Amorosi1, Soyeon Showman1,2
1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Summary:
Use of PacBio sequencing for characterizing barcoded libraries of genetic variants is on the rise. However, current approaches in resolving PacBio sequencing artifacts can result in a high number of incorrectly identified or unusable reads. Here, we developed a PacBio Read Alignment Tool (PacRAT) that improves the accuracy of barcode-variant mapping through several steps of read alignment and consensus calling. To quantify the performance of our approach, we simulated PacBio reads from eight variant libraries of various lengths and showed that PacRAT improves the accuracy in pairing barcodes and variants across these libraries. Analysis of real (non-simulated) libraries also showed an increase in the number of reads that can be used for downstream analyses when using PacRAT.
Availability And Implementation:
PacRAT is written in Python and is freely available (https://github.com/dunhamlab/PacRAT).
Supplementary Information:
Supplemental data are available at Bioinformatics online.
