RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes.

ABSTRACT: Numerous published genomes contain gaps or unknown sequences. Gap filling is a critical final step in de novo genome assembly, particularly for large genomes. While certain computational approaches partially address the problem, others have shortcomings regarding the draft genome's dependability and correctness (high rates of mis-assembly at gap-closing sites and high error rates). While it is well established that genomic repeats result in gaps, many sequence reads originating from repeat-related gaps are typically missed by existing approaches. A fast and reliable statistical algorithm for closing gaps in a draft genome is presented in this paper. It utilizes the alignment statistics between scaffolds, contigs, and paired-end reads to generate a Markov chain that appropriately assigns co

SUBMITTER: Midekso FD 

PROVIDER: S-EPMC9575681 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature