2-AIN-505, 2-AIN-251: Seminar in Bioinformatics (1), (3)
Winter 2023

Ryan R. Wick, Kathryn E. Holt. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol, 18(1):e1009802. 2022.

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Long-read-only bacterial genome assemblies usually contain residual errors, most 
commonly homopolymer-length errors. Short-read polishing tools can use short 
reads to fix these errors, but most rely on short-read alignment which is 
unreliable in repeat regions. Errors in such regions are therefore challenging to 
fix and often remain after short-read polishing. Here we introduce Polypolish, a 
new short-read polisher which uses all-per-read alignments to repair errors in 
repeat sequences that other polishers cannot. Polypolish performed well in 
benchmarking tests using both simulated and real reads, and it almost never 
introduced errors during polishing. The best results were achieved by using 
Polypolish in combination with other short-read polishers.