Results for "smith-waterman"
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MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
...rage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is wel...2898 days ago
CovCal: Coverage / Read Count Calculator
Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/configuration...2157 days ago
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 num...2346 days ago
xmatchview: smith-waterman alignment visualization
...e as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994) http://www.phrap.org) uses an implementation of the Smith-Waterman algorithm for comparing DNA s...2311 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...anning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to comput...2194 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.2164 days ago
RepeatMasker compatible blast tool
...t for custom matrices ( without KA-Statistics ). Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. Support fo...1967 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...ces. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust t...1930 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alig...1551 days ago
UniAligner: a parameter-free framework for fast sequence alignment
...equence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches, such as the Smith-Waterman algorithm, that work well for...49 days ago
