CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technologies paved the way t...paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlap...2094 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to cluste...ygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged re...2034 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, t...same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm that identifies CSBs in large...2029 days ago
RopeBWT2: Incremental construction of FM-index for DNA sequences
RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences....pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a m...2029 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of mi...sp;https://github.com/ncbi/SKESA/releases. Research Paper @ Link SKESA algorithm are as follows:...2009 days ago
RepeatMasker compatible blast tool
RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The...ty adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. Support for cross_match-lik...1985 days ago
BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et a...cantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately se...1982 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
OAT uses OrthoANI to measure the overall similarity betwe...genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species...d large comparison studies have demonstrated both algorithms to produce near identical re...1980 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single t...pret similarity pairs as edges of a network. A very efficient algorithm, based on the Disjoint S...1980 days ago
EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we pr...comparisons and analyses. Two of the core features are: a function prediction algorithm which is fully vectorized (ne...1979 days ago