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 f...2317 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...base error 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...2313 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become a...ithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing p...2311 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 quick...2164 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 betw...2155 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 tre...2130 days ago
EAGLER: a scaffolding tool for long reads.
...ads. 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 sho...2124 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...chnologies, 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...2144 days ago
WhatsHap: fast and accurate read-based phasing
...ds. 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 r...2131 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
.../minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./min...2108 days ago