Jit
Enthusiast computational biologist with business dream !!!
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InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
By Jit 1558 days agowww.interactivenn.net - InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 782 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...Comparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4792 days agobiochem218.stanford.edu - Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil Gopal3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 3202 days agogithub.com - This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...StringTie Transcript assembly and quantification for RNA-Seq
By Jit 2308 days agoccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...3D de novo assembly (3D DNA) pipeline
By Jit 2436 days agogithub.com - For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly. For the original version of the pipeline and to reproduce the...Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
By Jit 2317 days agosupport.10xgenomics.com - Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for...auN: a new metric to measure assembly contiguity
By Jit 1524 days agolh3.github.io - Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A...Pilon
By Rahul Nayak 3891 days agogithub.com - Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads...
