CoLoRMap: Correcting Long Reads by Mapping short reads
...igh-quality Illumina 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...2083 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
...2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged re...2023 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
...of genes that are consistently located close to each other, in the same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm that identifies CSBs in large...2017 days ago
RopeBWT2: Incremental construction of FM-index for DNA sequences
...incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a m...2017 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
...ompute resources. Source code for SKESA is freely available at https://github.com/ncbi/SKESA/releases. Research Paper @ Link SKESA algorithm are as follows:...1997 days ago
RepeatMasker compatible blast tool
...s ( without KA-Statistics ). Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. Support for cross_match-lik...1974 days ago
BLAST options, setting and defaults
...Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately se...1971 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
...ilarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species...cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical re...1969 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 sequ...to interpret similarity pairs as edges of a network. A very efficient algorithm, based on the Disjoint S...1969 days ago
EGAD: Ultra-fast functional analysis of gene networks
...n the guilt-by-association principle. These allow rapid controlled comparisons and analyses. Two of the core features are: a function prediction algorithm which is fully vectorized (ne...1967 days ago