The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program.Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments.
最近更新: 2年多前Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50.
最近更新: 2年多前NEMO: Nucleus for European Modelling of the Ocean is a state-of-the-art modelling framework for research activities and forecasting services in ocean and climate sciences
最近更新: 2年多前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
