Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm u...2245 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-...wly expressed transcripts. Scallop achieves this improvement through a novel algorithm t...2241 days ago
Metassembler: merging and optimizing de novo genome assemblies
Metassembler combines multiple whole genome de novo assemblies into a combined consensus...Genome assembly projects typically run multiple algorithms in an attempt to find the si...ngths and weaknesses. We present our metassembler algorithm t...2241 days ago
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,...2241 days ago
2218 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 algorithms.2210 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 u...2199 days ago
2234 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 genom...2234 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....2228 days ago