ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem. Perform correction of contigs using p...Tags: ONT, assembly, Illumina, polishing, pipeline
2318 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads. Racon is a great polishing tool th...Tags: Minipolish, tool, Racon, polishing, miniasm, assemblies
1578 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s interna...Tags: Merfin, improved, variant, filtering, assembly, evaluation, polishing, k-mer, validation
725 days ago
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version at https://arxiv.org/pdf/1902.04341.pdf More at&...Tags: Apollo, Sequencing, Technology, Independent, Scalable, Accurate, Assembly, Polishing, Algorithm
1474 days ago