HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns t...6.7-41.1% higher throughput than the existing algorithms while maintaining comparable...7% longer assembled contigs than the existing algorithms.2167 days ago
Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares the...s to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment...) of two sequences along their entire length. The algorithm uses a dynamic programming me...2156 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 genome assemblies u...2191 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral...relationships in the ancestor. Then a greedy algorithm is used to reconstruct the an...Computer simulation was used to validate the algorithm. We also applied the method t...2185 days ago
2182 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. If you want to use the old v...2160 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 ent...of non-model organisms. While algorithms are available that are speci...elop a transcriptome assembly algorithm that recovers alternatively s...e program that implements the algorithm is available at: http://facul...2142 days ago
2142 days ago
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 reference genome,...2139 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequen...unt. Memory- and time- efficient machine learning algorithms that address these shortcomi...machine learning-based long read error correction algorithm. The algorithm models every l...2094 days ago