npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing clust...2529 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
...a new de novo genome assembly project called Ra (https://github.com/mariokostelac/ra-integrate).Ra attempts to create de novo assemblies from raw nanopore and PacBio reads without requ...2514 days ago
Unicycler: Hybrid assembly pipeline for bacterial genomes
...ssemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm...2358 days ago
poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile s...enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package...2344 days ago
ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset ont...2344 days ago
IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
...to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It...g the statistics that we think will be useful for this task. However, nanopore sequencing is an emerging and...2344 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...or rate is similar to the raw input reads. So far miniasm is in early development stage. It has only been tested on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. In...2340 days ago
INC-Seq: accurate single molecule reads using nanopore sequencing
INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.2340 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available...ki/nanocorr) specifically for Oxford Nanopore reads, as existing packages w...thermore, the assembly with the long nanopore reads presents a much more co...2338 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
...Sim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The fi...2319 days ago