Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Homepage: URL: Keyword:chemĭescription: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
The code is free software, available under GNU-GPL license and the BigDFT developer community encourages anyone willing to contribute to join the team. The Poisson solver can also be downloaded and used independently and is integrated in ABINIT, Octopus and CP2K. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with explicit boundary conditions. The code BigDFT is available in ABINIT v5.5 and higher but can also be downloaded in a standalone version from the website.
GTH or HGH pseudopotentials are used to remove the core electrons. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). Homepage: URL: Keyword:physĭescription: BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set with the capability to use a linear scaling method. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput.
Jack Deslippe, Georgy Samsonidze, David A. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Description: The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
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