Jit
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pWhatsHap: a parallel, high-performance version of WhatsHap
By Jit 2203 days agobitbucket.org - Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in...Genome Annotation using MAKER tutorial !
By Shruti Paniwala 2166 days agowww.biostars.org - MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2129 days agoamos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...gEVAL: Genome Evaluation Browser
By Jit 1987 days agogeval.sanger.ac.uk - The gEVAL Browser allows the evaluation of genome assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assist in...De novo Genome Assembly for Illumina Data
By Rahul Nayak 1771 days agowww.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...Synteny and Rearrangement Identifier (SyRI)
By Jit 1665 days agoschneebergerlab.github.io - SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI...Genome assembly training tutorial at Galaxy !
By Jit 1429 days ago Comments (1)training.galaxyproject.org - In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance, now classic works by Holly Wichman and Jim Bull (Bull 1997, Bull...QuasiModo - Quasispecies Metric Determination on Omics
By Neel 1248 days agogithub.com - This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each...
