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SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 141 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial...
By Jit 2820 days agobitbucket.org - MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome...Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive...
By Jit 2474 days agowww.zbh.uni-hamburg.de - Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1762 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...DarkHorse
By Jit 3077 days agodarkhorse.ucsd.edu - 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...NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).
By Poonam Mahapatra 4122 days agoThe 4-day course is organized as a series of morning lectures and afternoon hands-on workshops.
Useful Publications and Websites for Deep Sequencing Data Analysis
Last updated 3983 days ago by Rahul NayakGlobal overview papers Next generation quantitative genetics in plants. Jiménez-Gómez, Frontiers in Plant Science 2:77, 2011 Full Text [equally relevant to animal and microbial systems] Sense from sequence reads: methods for...GABi
GABi Research The major researching fields defined as the GABi scope are described next: Sequence Analysis Protein Structure Prediction Comparative Genomics Functional Analysis of Residues on Protein Families Gene/Protein...Managing and Analyzing Next-Generation Sequence Data
By Rahul Agarwal 3851 days agowww.ploscompbiol.org - Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental...-
Next generation sequencing in R or bioconductor environment
Last updated 3828 days ago by John Parker Comments (3)There are many R software and bioconductor packages for NGS data analysis, some of them are as follows Biostrings The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It...
