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
LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 2208 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 2208 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 2210 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 2214 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 2214 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.htmlFree Genomics data !
By BioStar 2218 days agowww.darwintreeoflife.org - The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane...MEC: Contig Misassembly Correction
By BioStar 2221 days agogithub.com - MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on...Tadpole: an assembler, error-corrector, and read-extender
By BioStar 2221 days agojgi.doe.gov - Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and therefore, is not particularly good for diploid organisms. Tadpole is...QuorUM: An Error Corrector for Illumina Reads
By BioStar 2221 days agowww.genome.umd.edu - We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is...Musket - a multistage k-mer spectrum based corrector
By BioStar 2221 days agomusket.sourceforge.net - Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...
