Open-source foundation of the user-sponsored PyMOL molecular visualization system.
最近更新: 2年多前NAMD: A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
最近更新: 2年多前The OpenLB project provides a C++ package for the implementation of lattice Boltzmann methods that is general enough to address a vast range of tansport problems, e.g. in computational fluid dynamics. The source code is publicly available and constructed in a well readable, modular way. This enables for a fast implementation of both simple academic test problems and advanced engineering applications.
最近更新: 2年多前A set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.
最近更新: 2年多前Redundans pipeline assists an assembly of heterozygous genomes. Program takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly.
最近更新: 2年多前Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. The method is designed for rapid analysis on standard compute hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, and most WGS tumor/normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in small sets of diploid samples and somatic variants in matched tumor/normal sample pairs. There is experimental support for analysis of unmatched tumor samples as well (see details below). Manta accepts input read mappings from BAM or CRAM files and reports all SV and indel inferences in VCF 4.1 format.
最近更新: 2年多前FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.
最近更新: 2年多前Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome assembly. Currently, Flye will produce collapsed assemblies of diploid genomes, represented by a single mosaic haplotype. To recover two phased haplotypes consider applying HapDup after the assembly.
最近更新: 2年多前rMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of rMATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, rMATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. rMATS handles replicate RNA-Seq data from both paired and unpaired study design.
最近更新: 2年多前
