PolishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

ABSTRACT: Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best pract

SUBMITTER: Chang J 

PROVIDER: S-EPMC9985148 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature