Many-to-many pairwise alignments of two sequence sets
...ment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming method to ensure the alignment is op...2139 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, in...2175 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
...CAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of gene...uter simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral...2168 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.2138 days ago
2125 days ago
mmgenome: Tools for extracting individual genomes from metagneomes
...The mmgenome R package also facilitates effortless integration with additional data sources and hence should not be seen as "yet another binning method", but rather a package to int...2088 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
...graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and...2087 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...e recent developments in long reads sequencing methods offer a promising way to add...in long reads.We introduce CoLoRMap, a hybrid method for correcting noisy long rea...compares well with existing hybrid correction methods.The source code of CoLoRMap...2077 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing mult...2073 days ago
LoRMA: A tool for correcting sequencing errors in long reads
An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs wit...ccording to our experiments, the proposed method is the most accurate one rely...2060 days ago