BioStar
Bioinformatician
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- BioStar on Sibelia: A comparative genomics tool (1955 days ago): Basic usage =========== In this manual it is assumed that "Sibelia" is...
- BioStar on AutoDock Vina: an open-source program for doing molecular docking. (2092 days ago): AutoDockFR (or ADFR in short) is a protein-ligand docking...
- BioStar on AutoDock Vina: an open-source program for doing molecular docking. (2092 days ago): QVina-W, a new docking tool particularly useful for wide search space,...
- BioStar on Nextflow: Data-driven computational pipelines (2206 days ago): A Review of Scalable Bioinformatics Pipelines by Bjørn Fjukstad &...
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reads, genome, assembly, data, tool, sequence, sequencing, genomic, analysis, package, pipeline, Correction, Gene, Illumina, Breeding, Bioinformatics, Automated, learn, web, alignment, sequences, accurate, program, R, DNA, long, server, tools, Annotation, metagenomics, genomes, Visualization, graph, error, ngs, PacBio, Ontology, RNA, biological, generation, open-source, software, Genomics, Hi-C, RNA-seq, tree, python, Training, identification, genes
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BioStar's bookmarks
medaka: Sequence correction provided by ONT Research
By BioStar 2117 days agogithub.com - medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2132 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation...
By BioStar 2154 days agowego.genomics.org.cn - WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...CSAR-web: a web server of contig scaffolding using algebraic rearrangements
By BioStar 2156 days agogenome.cs.nthu.edu.tw - CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. CSAR-web can...Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
By BioStar 2157 days agogithub.com - Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly,...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 2169 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
By BioStar 2181 days agogithub.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...Kubernetes: open-source system for automating deployment, scaling, and management of containerized...
By BioStar 2206 days agohttps://kubernetes.io/ - It groups containers that make up an application into logical units for easy management and discovery. Kubernetes builds upon 15 years of experience of running production workloads at Google, combined with best-of-breed ideas and practices from...Nextflow: Data-driven computational pipelines
By BioStar 2206 days ago Comments (2)https://www.nextflow.io/ - Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Its fluent DSL simplifies the implementation and the deployment of...pbmm2:A minimap2 frontend for PacBio native data formats
By BioStar 2208 days agogithub.com - pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for...
