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Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2354 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...LRSDAY: Long-read Sequencing Data Analysis for Yeasts
By Poonam Mahapatra 2049 days agogithub.com - Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding...Comparative Genomics Data Set Including 240 Mammals Released !
By Jit 1598 days agoThe genome of 130 mammals was sequenced by a large international consortium and the data was analyzed together with 110 existing genomes to allow scientists to identify the important positions in the DNA.AMR Database !
By LEGE 305 days agogithub.com - ARG-ANNOT. PMID: 24145532 CARD. PMID: 23650175 MEGARes PMID: 27899569 NCBI BioProject: PRJNA313047 plasmidfinder PMID: 24777092 resfinder. PMID: 22782487 VFDB. PMID: 26578559 SRST2's version...Mash: fast genome and metagenome distance estimation using MinHash
By Jit 2671 days agogithub.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...RNA-Seq Data Pathway and Gene-set Analysis Workflows
By Jit 4180 days agoDescribe the GAGE workflows on RNA-Seq data pathway analysis and gene-set analysis.Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 2524 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 1887 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...Encode sequencing data freely available to download and use for academic means
By Rahul Agarwal 4041 days ago Comments (3)genome.ucsc.edu - In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed...deepTools
By Martin Jones 3801 days agoUser-friendly tools for the normalization and visualization of deep-sequencing data
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