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 re...2143 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to trade...unt. Memory- and time- efficient machine learning algorithms that address these shortcomi...machine learning-based long read error correction algorithm...2098 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technologies paved the way to an exceptional increase in the...paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm...2098 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 clustering and assembling short reads...ygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm...2038 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, that can also be executed via com...same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm...2033 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. It works by incrementally insert...pseudo-BWT position by position, starting from the end of the sequences. This algorithm...2032 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using...sp;https://github.com/ncbi/SKESA/releases. Research Paper @ Link SKESA algorithm...2012 days ago
RepeatMasker compatible blast tool
RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this...ty adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm...1989 days ago
BLAST options, setting and defaults
BLAST stands for Basic Local Alignment 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...1986 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species...d large comparison studies have demonstrated both algorithm...1984 days ago