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
2353 days ago
Tags: MashMap, fast, approximate, software, mapping, long, reads, PacBio, ONT, assembly, reference, genome(s)
2333 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
2190 days ago
Tags: MARVEL, assembler, Assembly, Genome, ONT, Nanopore, PacBio
2190 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
2166 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
2108 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
2023 days ago
Tags: SViper, Swipe, Structural, Variants, ONT, PacBio, reads, Illumina
1594 days ago
Tags: Nanopore, adapters, Porechop, Clean, ONT
1551 days ago
medaka: Sequence correction provided by ONT Research
medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive w...Tags: medaka, Sequence, correction, ONT, Research, nanopore
1445 days ago