17th November 2016
The long sequencing reads produced by Oxford Nanopore’s platforms enable the assembly of genomes with superior contiguity compared to those produced by second generation technologies. In some circumstances it can be beneficial to polish the assembled contigs using short or long reads, to correct smaller indels and substitutions, hence improving the overall assembly quality (Koren et al.; Vaser et al.). In order to make this process more accessible we have constructed an assembly polishing pipeline, which integrates the canu long read assembler with the long-read only racon polishing tool and the Pilon tool tailored for polishing using short Illumina reads. Evaluation of the pipeline on simulated data indicates that using only long reads for polishing by racon can improve significantly the contig accuracy, and using both polishing approaches can provide very accurate results.