MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a reference...and thus speed-up genome finishing. The proposed algorithm builds an extension graph whe...maximizes the cumulative contig length. The Mix algorithm...2209 days ago
2186 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns the long re...ain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable...-60.7% longer assembled contigs than the existing algorithm...2177 days ago
Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares them all to one or more sequences,...s to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment...) of two sequences along their entire length. The algorithm...2167 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of geno...2202 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic ord...ssor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the an...ies. Computer simulation was used to validate the algorithm...2195 days ago
2193 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm...2171 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study entire...mes of non-model organisms. While algorithms are available that are speci...develop a transcriptome assembly algorithm that recovers alternatively s...tware program that implements the algorithm...2153 days ago
2153 days ago