Jit
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Roary: the Pan Genome Pipeline
By Jit 2165 days ago Comments (1)sanger-pathogens.github.io - Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of...PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
By LEGE 309 days agogithub.com - What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs...Webinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016
By Yeshodari 3247 days agoLive Webinar on Streamlining large scale NGS data analysis using the Strand NGS Pipeline Manager on 24 Feb 2016 Abstract: Strand NGS includes comprehensive workflows for DNA-Seq, RNA-Seq, Small RNA-Seq, ChIP-Seq, MeDIP-Seq, and Methyl-Seq analysis....ONT assembly and Illumina polishing pipeline
By Jit 2590 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...ARC: pipeline which facilitates iterative, reference guided de novo assemblies
By Jit 2345 days agoibest.github.io - ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble...CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS...
By BioJoker 2088 days agowww.nature.com - Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs. https://www.nature.com/articles/nm.3975DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 1797 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...sunbeam: A robust, extensible metagenomics pipeline
By Jit 1652 days agogithub.com - Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1383 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1112 days agoGenome assembly pipeline !
