PTAssembler

PTAssembler: Open-Source Software for Assembling Nanopore Sequencing Data

PTAssembler is an open-source software for assembling nanopore sequencing data. It is designed to handle the high error rate and long reads produced by nanopore sequencing platforms such as those from Oxford Nanopore Technologies.

What is PTAssembler?

PTAssembler is an open-source software tool specifically designed for assembling nanopore sequencing data. Nanopore sequencing platforms like those from Oxford Nanopore Technologies produce long sequencing reads (tens to hundreds of kilobases) but have a high per-base error rate compared to other next-generation sequencing technologies.

PTAssembler implements a pipeline that is optimized to handle these long, erroneous nanopore reads. Key steps include read error correction with multiple sequence alignment to generate consensus reads, pairwise overlap detection, and construction of a string graph from the overlaps. The string graph is simplified and ultimately converted into contigs using standard de Bruijn graph techniques.

Some advantages of PTAssembler include the ability to handle reads over 1 million bases long, high consensus accuracy from its multiple sequence alignment error correction approach, and improved handling of repetitive genomic regions because of the long reads. It is written in C++ and Python and runs on Linux systems. PTAssembler enables high-quality genome assemblies to be constructed entirely from nanopore sequencing data.

PTAssembler Features

Official Links