PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment
| Autor: | Chiann-Ling C. Yeh, Maitreya J. Dunham, Soyeon Showman, Clara J. Amorosi |
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| Rok vydání: | 2021 |
| Předmět: |
Statistics and Probability
Multiple sequence alignment Downstream (software development) Computer science Genetic variants High-Throughput Nucleotide Sequencing Variant allele Computational biology Sequence Analysis DNA Python (programming language) Barcode Biochemistry Applications Notes Computer Science Applications law.invention Computational Mathematics Computational Theory and Mathematics law Molecular Biology computer Sequence Alignment Algorithms Software computer.programming_language |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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