2563 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapp...2522 days ago
phyloXML: XML for evolutionary biology and comparative genomics
...events. Using these standardized elements allows interoperability between various applications and databases. Furthermore, both due to extensible nature of XML itself and the provisi...2346 days ago
Recovery of complete genomes from metagenomes
...omes Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen Nature Biotechnology 2013, doi: ...2319 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
...ty and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation. https://www.nature.com/articles/nmeth.45562305 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
...andoc!) Please cite: Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, doi: 10.1038/n...2233 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
...nd paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization. Scallop paper has been published at Nature Biotechnology. The datasets a...2187 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...ity of assembled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON. https://www.nature.com/articles/nmeth.44322184 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...atwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology 2013 Dec;31(12)...2181 days ago
mScaffolder: A comparative genome scaffolding tool
...e guided by their alignments to the reference genome. Please send your questions and comments to mchakrab@uci.edu. Citation https://www.nature.com/articles/s41588-017-0010-...2149 days ago