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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.
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.
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.
Generates statistical data summaries for long read sequencing data. NanoStat computes various statistics from an Oxford Nanopore dataset in three different formats. The application compiles general statistics about the studied dataset. It also contains the number of reads and fraction above quality cutoffs as well two ranking tables presenting the five more importants: (i) read lengths and their average base call quality score and (ii) average base call quality scores and their read lengths. The script is part of the NanoPack toolkit.
cwDTW / Continuous Wavelet Dynamic Time Warping for unbalanced global mapping of two signals
Provides a continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing. cwDTW handles the unbalanced global mapping between two ultra-long signal sequences via the algorithm based on continuous wavelet transform (CWT). Picks are selected from CWT sequences to create form feature sequences. This method is also useful for different nanopore sequencing tasks, such as base calling, reads mapping, variant identification, and methylation detection.
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.
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