![]() ![]() cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Homepage: URL: ĭescription: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. CEGMA source code, compiled binaries and documentation are available under the GNU GENERAL PUBLIC LICENSE. The system includes the use of a profile for each core gene to ensure the reliability of the final predicted gene structure. It then proposes and redefines gene structures using a iterative combination of GeneWise, HMMER and geneid. The procedure uses information from the core genes of six model organisms by first using TBLASTN to identify candidate regions in a new genome. We define a set of 458 core proteins, and the protocol, CEGMA, to find orthologs of the core proteins in new genomes and to determine their exon-intron structures. We use the KOGs database to build a set of these highly conserved ubiquitous proteins. ![]() The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes. Homepage: URL: ĭescription: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. If you use Kraken 2 defaults, specify 35 as the kmer length. If you use Kraken 1 defaults, specify 31 as the kmer length. However, the default kmer length is different depending on the version of Kraken used. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. 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. ![]()
0 Comments
Leave a Reply. |