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.2156 days ago
Many-to-many pairwise alignments of two sequence sets
...l sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming me...2145 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 asse...2180 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...2174 days ago
2171 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 version, it can be...2149 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...availability of de novo assembly algorithms, it is feasible to study ent...es of non-model organisms. While algorithms are available that are speci...develop a transcriptome assembly algorithm that recovers alternatively s...ware program that implements the algorithm is available at: http://facul...2131 days ago
2131 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 refere...2128 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...technology into account. Memory- and time- efficient machine learning algorithms that address these shortcomi...Hercules, the first machine learning-based long read error correction algorithm. The algorithm models every l...2083 days ago