Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...NA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available...urtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages w...hermore, the assembly with the long nanopore reads presents a much more co...2350 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, 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...2331 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 a...2203 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...2194 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...at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with...2169 days ago
EAGLER: a scaffolding tool for long reads.
...The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads. The tool should be co...2163 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single lapt...2156 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...ogies, including but not limited to: NGS short reads (Illumina HiSeq) clone-based sequencing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X Genomics Linked-Re...2183 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2174 days ago
WhatsHap: fast and accurate read-based phasing
...Features Very accurate results (Martin et al., WhatsHap: fast and accurate read-based phasing) Works well with Illumina, PacBio, Oxford Nanopore and other types of reads It...2170 days ago