Jit
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YAMP: Yet Another Metagenomic Pipeline
By BioStar 819 days agogithub.com - YAMP is constructed on Nextflow, a framework based on the dataflow programming model, which allows writing workflows that are highly parallel, easily portable (including on distributed systems), and very flexible and customisable,...Webinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016
By Yeshodari 3893 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....Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
By Jit 3236 days agosourceforge.net - Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the...ARC: pipeline which facilitates iterative, reference guided de novo assemblies
By Jit 2991 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 2734 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.3975HaploTypo: a variant-calling pipeline for phased genomes
By Jit 2480 days agogithub.com - An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2423 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
By BioStar 2242 days agogithub.com - PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 2029 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 1758 days agoGenome assembly pipeline !
