BioStar
Bioinformatician
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- BioStar on Sibelia: A comparative genomics tool (1485 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. (1622 days ago): AutoDockFR (or ADFR in short) is a protein-ligand docking...
- BioStar on AutoDock Vina: an open-source program for doing molecular docking. (1622 days ago): QVina-W, a new docking tool particularly useful for wide search space,...
- BioStar on Nextflow: Data-driven computational pipelines (1736 days ago): A Review of Scalable Bioinformatics Pipelines by Bjørn Fjukstad &...
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reads, genome, assembly, data, tool, sequence, sequencing, analysis, package, pipeline, genomic, Correction, Gene, Illumina, Breeding, Bioinformatics, Automated, learn, sequences, accurate, web, program, R, DNA, long, server, tools, alignment, Annotation, metagenomics, genomes, Visualization, error, ngs, PacBio, Ontology, RNA, biological, generation, open-source, software, Genomics, Hi-C, RNA-seq, tree, python, Training, identification, genes, free
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BioStar's bookmarks
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 1699 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 1711 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 1736 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 1736 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 1738 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...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1738 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...SeqMule: Automated human exome/genome variants detection
By BioStar 1738 days agodoc-openbio.readthedocs.io - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1740 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...Sequanix: a dynamic graphical interface for Snakemake workflows
By BioStar 1744 days agogithub.com - A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats). A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable...Biological databases !
By BioStar 1744 days ago Comments (4)ftp.ncbi.nih.gov - Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ... ftp://ftp.ncbi.nih.gov/genomes/ https://hgdownload.soe.ucsc.edu/downloads.html
