Results for "Long"
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GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. Consistently very high sensitivity and precision ...Tags: GraphMap, sensitive, accurate, mapper, long, error-prone, reads
2515 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. I...Tags: Ultrafast, de novo, assembly, long, noisy, reads, consensus
2342 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)
2326 days ago
LAMSA: fast split read alignment with long approximate matches
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes takes the advantage of the rareness of SVs to implement a specifi...Tags: LAMSA, fast, split, read, alignment, long, approximate, matches
2173 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.Tags: minialign, fast, accurate, alignment, tool, PacBio, Nanopore, long, reads
2164 days ago
EAGLER: a scaffolding tool for long reads.
EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of 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 Nano...Tags: EAGLER, scaffolding, tool, long, reads, genome, assembly
2153 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., & Bafna, V. (...Tags: Cerulean, hybrid, assembly, short, long, reads, pacbio, nanopore
2152 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats i...Tags: HALC, algorithm, long, read, error, correction, NGS, PacBio, Nanopore
2149 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA m...Tags: SALSA, tool, scaffold, long, read, assemblies, Hi-C, Genome
2142 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect...Tags: ReMILO, reference, assisted, misassembly, detection, algorithm, short, long, reads
2121 days ago
