GIGGLE: a search engine for large-scale integrated genome analysis
...al files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the access...2306 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phyloge...2266 days ago
Protein Subcellular Localization Prediction
...and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and laborious experimental methods. http://abi.inf.uni-tuebinge...2256 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One...848 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
...ene/Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-...2188 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...lotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific...2181 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...on 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Ghur...2150 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...ragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to addr...sets show that CoLoRMap compares well with existing hybrid correction methods.The source code of CoLoRMap i...2084 days ago
LRCstats: a tool for evaluating long reads correction methods
...which can cause issues in downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short read...2082 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
...e. It is the "right sequence" you want, and now the only way to get it is to produce way too many assemblies on a good RNA data set, with several methods and several parameter setting...2042 days ago