AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using...2223 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo o...Nanopore to (large) reference genomes. It was designed to quickly and correctly al...ad and then a banded Smith-Waterman alignment algorithm to compute the final align...2215 days ago
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 algori...2205 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-e...owly expressed transcripts. Scallop achieves this improvement through a novel algori...2202 days ago
Metassembler: merging and optimizing de novo genome assemblies
Metassembler combines multiple whole genome de novo assemblies into a combined consensus a.... Genome assembly projects typically run multiple algorithms in an attempt to find the si...engths and weaknesses. We present our metassembler algori...2202 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 g...n and thus speed-up genome finishing. The proposed algorithm builds an extension graph whe...t maximizes the cumulative contig length. The Mix algori...2202 days ago
2179 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 rea...tain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable...4-60.7% longer assembled contigs than the existing algori...2171 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, w...ts to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment...s) of two sequences along their entire length. The algori...2160 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 ge...2195 days ago