Search Results for "nanopore"
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Showing 12 open source projects for "nanopore"
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PyNanoLab
data analysis and Visualization with matplotlib
PyNanoLab contains a variety of tools to complete the data analysis, statistics, curve fitting, and basic machine learning application. Visualization in pynanolab is based on matplotlib. The setup tools is desinged to control and set-up all the details of the figure with a GUI. -
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PoreMeth
PoreMeth is a tool for the identification of DMRs from Nanopore data.
PoreMeth is a tool for the detection of differentially methylated regions (DMRs) from nanopore sequencing data of two samples. PoreMeth tool is based on a heterogeneous form of the shifting level model, which integrates distances between consecutive CpGs in the segmentation algorithm. PoreMeth is fed with ∆β values and generates genomic segments with increased (hyper-) or decreased (hypo-) methylation levels between two samples, which are then evaluated for statistical significance using the Wilcoxon-rank sum test. -
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pycoQC
pycoQC computes metrics and generates Interactive QC plots
PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. PycoQC relies on the sequencing_summary.txt file generated by Albacore and Guppy, but if needed it can also generate a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices and basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. -
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NanoR
R package built to analyze and compare Nanopore data
NanoR is a package for the statistical language and environment R, tested on Unix, MacOSX and Windows, that allows user-friendly analysis and comparison of 1D MinION and GridION X5 sequencing data within acceptable time frames. -
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NanoGLADIATOR
Real-time detection of copy number alterations from nanopore data.
Nano-GLADIATOR is a novel software tool that allows to analyze WGS data generated during a MinION or GridION X5 run for the detection of copy number alterations (CNAs). Nano-GLADIATOR (Nanopore Genomic aLterations AnD allelIc frAcTiOn pRedictor) is capable to perform CNVs/CNAs detection and allelic fraction prediction during the sequencing run ("On-line" mode for real time molecular karyotyping) and once the experiment is completed ("Off-line" mode, for parallel analysis of multiple samples). In "On-line" mode the tool must be launched simultaneously to a nanopore experiment so that, by exploiting the data flow generated during the sequencing process, it can perform real-time CNVs/CNAs detection. ... -
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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R_poRe
An R package to enable visualisation of nanopore sequencing data
The Oxford Nanopore MinION is a revolutionary sequencer with a unique model of data delivery, requiring novel tools for the novice user. This package enables organisation and visualisation of MinION data on the MinION laptop -
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Opera
An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads. An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes. Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large,... -
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Sparc: a consensus algorithm for PacBio/Nanopore data Manuscript can be found: https://peerj.com/preprints/1401.pdf
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NanoID
IV and PSD characterization of a nanopore
IV and PSD characterization of a nanopore -
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NanoFabricator
Create Nanopore with this Labview program
I [solely] invented a method to fabricate nanopore. It is to simply applying a hgih voltage across the membrane. This is the program to do the job. -
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ReadSim
Simple reads simulator for pacbio & nanopore
Simple reads simulator for pacbio & nanopore
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