CAR: Reconstructing Contiguous Regions of an Ancestral Genome
We describe a new method for predicting the ancestral order and orientation of those int...onably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed a...2556 days ago
AVID: A Global Alignment Program
A new global alignment method called AVID. The method is designed to be fast, memory effic...methods for their comparison. These formats and methods should be useful for future studies. The tools we have de...2550 days ago
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome su...acilitate extensions for new functions and incorporation of new tools in the future. Availability and Implementa...2376 days ago
Recovery of complete genomes from metagenomes
This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as describ...e W. Tyson, Kåre L. Nielsen and Per .H. Nielsen Nature Biotec...2333 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementat...the current implementation of the rectangle graph approach in SPAdes, in the future we plan to integrate RGM in S...2332 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein sequence sets. MMs...ive protein sequence searching for the analysis of massive data sets. Nature Biotec...2248 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-exon...age deviation minimization. Scallop paper has been published at Nature Biotec...2201 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 ge...ng of de novo genome assemblies based on chromatin interactions. Nature Biotec...2195 days ago
2081 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more gen...Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotec...1956 days ago