Jit
Enthusiast computational biologist with business dream !!!
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3D de novo assembly (3D DNA) pipeline
By Jit 2435 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...ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 878 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...Hagfish - assess an assembly through creative use of coverage plots
By Abhi 3787 days agogithub.com - Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 3230 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 2085 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 2463 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 3073 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 3064 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...Phased Human Genome Assembly !
By Rahul Nayak 2917 days agoDiploid Assembly of a Puerto Rican Female Adds a Rich Resource to Population-Specific Reference GenomesRa assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 3201 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...
