Results for "Bioinformatics"
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In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would not have been possible without the help of many people who directly or indirectly contributed to its development. ...Tags: Bioinformatics, Analysis, Visualization, Platform, Omics, NGS, Anvio
2888 days ago
- statistical analysis and visulization of functional profiles for genes and gene clustersBioconductor version: Release (3.3)This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.Author: Guangchuang Yu <guangchuangyu at gmail.com>...
Tags: Bioinformatics, clusterProfiler, GO, R, Package, Omics, Genes, Cluster
2888 days ago
- The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting m...
Tags: Bioinformatics, Greengenes database, Bacteria, Archaea
2875 days ago
- DarkHorse is a bioinformatic method for rapid, automated identification and ranking of phylogenetically atypical proteins on a genome-wide basis. It works by selecting potential ortholog matches from a reference database of amino acid sequences, then using these matches to calculate a lineag...
Tags: Bioinformatics, HGT, Genes, Horizontal, Transfer, Method, Tools, DarkHorse
2882 days ago
- KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each...
Tags: Bioinformatics, Analysis, NGS, KISSPLICE, Transcriptome, Assembler, Genome
2827 days ago
- Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically...
Tags: Bioinformatics, NearHGT, Horizontal, Gene, Transfer, Haifa
2882 days ago
Linux command line exercises for NGS data processing
The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory (cd) to the linuxTutorial folder, and do all the processing inside: [uzi@qui...Tags: Bioinformatics, Tutorial, Genome, NGS, Pipelines
2882 days ago
- SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions 1.0: May 30, 2013: First public release on biobits.org. 1.1: July 24, 2013: Updated wi...
Tags: Bioinformatics, NGS, Sequence, Samtools, Primer, Tutorial
2881 days ago
- Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors...
Tags: Bioinformatics, NGS, Reads, Silulator, INDEL, SNPs, Simulation
2881 days ago
- _A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_. Point to note: There are many situations where A5-miseq is not the right tool for the job. In order to produce ...
Tags: Bioinformatics, Analysis, NGS, A5-miseq, NGOPT Assembler, Genome
2825 days ago
