IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It includes a functions to generate a number plots for examining the statistics that we think will be useful for this task. However, nanopore sequencing is an emergi...Tags: tools, quality, assessment, Oxford, Nanopore, MinION, sequencer, IONiseR, R
2398 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make...Tags: Oxford, Nanopore, Sequencing, Hybrid, Error, Correction, de novo, Assembly, Eukaryotic, Genome
2393 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware...Tags: NGMLR, long-read, mapper, designed, align, PacBio, Oxford, Nanopore
2246 days ago
Porechop: tool for finding and removing adapters from Oxford Nanopore reads
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapte...Tags: Porechop, tool, finding, remove, adapters, Oxford, Nanopore, reads, ONT, NGS, Long
2212 days ago
Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb&n...Tags: Wtdbg2, de novo, sequence, assembler, long, noisy, reads, PacBio, Oxford, Nanopore, ONT
2069 days ago
Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplex...Tags: Deepbinner, signal-level, demultiplexer, Oxford, Nanopore, reads
2030 days ago
Tags: Katuali, flexible, consensus, pipeline, Snakemake, basecall, assemble, polish, Oxford, Nanopore, Technology, sequencing, data
1974 days ago
Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porecho...Tags: Deepbinner, signal-level, demultiplexer, Oxford, Nanopore, reads, adaptor
1590 days ago
orthodotter: Synteny plots (oxford grid)
orthodotter -h -------------------------------------------------------------------------------- orthodotter - Plot orthologous genes on an oxford grid. -f <file> : input file, containing orthologous genes, default is stdin species chr-name start end spe...Tags: orthodotter, Synteny, plots, oxford, grid
2505 days ago