Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

INC-Seq: accurate single molecule reads using nanopore sequencing

BACKGROUND Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read error rates (>10 %), including RNA-seq, haplotype sequencing and 16S sequencing. RESULTS We developed the Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) as a stra...

Error correction and assembly complexity of single molecule sequencing reads

Third generation single molecule sequencing technology is poised to revolutionize genomics by enabling the sequencing of long, individual molecules of DNA and RNA. These technologies now routinely produce reads exceeding 5,000 basepairs, and can achieve reads as long as 50,000 basepairs. Here we evaluate the limits of single molecule sequencing by assessing the impact of long read sequencing in...

Local Alignment Refinement Using Structural Assessment

Homology modeling is the most commonly used technique to build a three-dimensional model for a protein sequence. It heavily relies on the quality of the sequence alignment between the protein to model and related proteins with a known three dimensional structure. Alignment quality can be assessed according to the physico-chemical properties of the three dimensional models it produces. In this w...

Fast and sensitive mapping of nanopore sequencing reads with GraphMap.

Realizing the democratic promise of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. Here we present GraphMap, a mapping algorithm designed to analyse nanopore sequencing reads, which progressively refines candidate alignments to robustly handle potentially high-error rates and a fast graph traversal to align long rea...

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads