MinION real-time data analysis software tools | Whole-genome sequencing
The recently released Oxford Nanopore MinION sequencing platform presents many innovative features opening up potential for a range of applications not previously possible. Among these features, the ability to sequence in real-time provides a unique opportunity for many time-critical applications.
Allows to evaluate the sequencing process in real time by extracting reads, while the samples are being sequenced on the MinION device, and show streaming plots through a graphical user interface (GUI) with quality statistics of the run. minoTour provides pore/channel activity and percentage of coverage and average depth in presence of a reference sequence and allows to eject molecules in real time if they are not from the target genome of interest with the ‘Read Until’ approach.
An open-source software package to facilitate real-time analysis of MinION sequencing data. npReader can simultaneously extract sequence reads and stream them to downstream analysis pipelines while the samples are being sequenced on the MinION device. It provides a command line interface for easy integration into a bioinformatics work flow, as well as a graphical user interface which concurrently displays the statistics of the run. It also provides an application programming interface for development of streaming algorithms in order to fully utilize the extent of nanopore sequencing potential.
Allows users to make comparisons between several runs of Oxford Nanopore alignments and sequencing data. Nanocomp is a standalone application that permits users to create informative quality control (QC) graphs. It is able to perform comparison across barcodes or runs of read length and quality distributions, number of reads, throughput and reference identity. The script is part of the NanoPack toolkit.
Allows users to perform real-time selective sequencing. RUBRIC enables alignment against conventional nucleic acid references to provide the basis for sequence/reject decisions. This tool is designed for working with different computing resources typical of portable. It can pre-screen features that seek to admit only informative and timely reads to the decision process, reducing computational requirements.
Offers a set of scripts and modules dedicated to the processing and the visualization of long read sequencing data. NanoPack consists of five mains components: (i) NanoPlot, that allows the generation of plots and statistical summaries, (ii) NanoComp, for several runs comparisons, (iii) NanoStat, that generates statistical summaries from various inputs; (iv) NanoFilt, that sorts files based on a minimum length and minimum quality cut-off, (v) and NanoLyse, that offers a method for removing reads mapping to the lambda phage genome.
Provides method for the quality assessment of Oxford Nanopore MinION data. IONiseR is an R package that extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.
Offers a method for long read sequencing data filtering and trimming. NanoFilt is a Python script that performs its filtering based on mean read quality and GC content and read length. The application also includes a functionality that permits users to perform trimming tasks with a customized number of nucleotides from either read ends. The program can be embedded in existing pipelines prior to alignment and have a minimal memory footprint. The script is part of the NanoPack toolkit.