Results for "ONT"
Tags
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 onto the contigs obtained in the previous steps using BWA mem. Perform correction of contigs using p...Tags: ONT, assembly, Illumina, polishing, pipeline
2338 days ago
- When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the options: spades.py This produces: SPAdes genome ...
Tags: SPAdes, hybrid, genome, assembly, ONT, Nanopore
2334 days ago
- MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but...
Tags: MashMap, fast, approximate, software, mapping, long, reads, PacBio, ONT, assembly, reference, genome(s)
2318 days ago
Bioinformatics tools developed for Oxford Nanopore data analysis !
MinION is the only portable real-time device for DNA and RNA sequencing. Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. One of the technical advantage...Tags: Bioinformatics, tools, developed, Oxford, Nanopore, analysis, ONT
2303 days ago
What are the best software options available for nanopore (ONT) reads ?
Tags: ONT, Nanopore, Assembly, Sequencing, Reads, fast
2175 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repe...Tags: Flye, de novo, assembler, ONT, Nanopore, PacBio, Assembly, single, molecule, sequencing, reads
2175 days ago
- MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap (again) scrubbing assembly graph construction and touring o...
Tags: MARVEL, assembler, Assembly, Genome, ONT, Nanopore, PacBio
2175 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
2151 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below). Quickst...Tags: Nanopolis, polish, ONT, nanopore, genome, assembly, ngs
2093 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
2008 days ago
