repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
...lds). The join between two contigs A and B is considered correct if: Their relative orientation is correct Their relative order is correct The gap estimate is similar to the tr...2289 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...lignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps le...2254 days ago
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Many-to-many pairwise alignments of two sequence sets
...eman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along thei...m the scoring matrix, minus penalties arising from opening and extending gaps in the aligned sequences. Th...2199 days ago
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BLAST options, setting and defaults
...se Notes BLASTNBLASTPBLASTXTBLASTNTBLASTXPSIBLAST Gap opening penalty:cost to open a gap [integer] default = 5 defau...no default Supported and Suggested Values for Gap Open and Extension in BLASTP,...2025 days ago
HumCFS: a database of fragile sites in human chromosomes
...en recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chromosomal re-arrangement. There is large gap in our knowledge of human CFS...1893 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Lin...IX command lines. They compare the performance of gapFinisher against two other pub...1615 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied specie...piled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read...1504 days ago