Jit
Enthusiast computational biologist with business dream !!!
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DeCoSTAR - Detection of Co-evolution
By Jit 2785 days agopbil.univ-lyon1.fr - DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.Ancestral genes or domains are deduced from...
Evaluation of genome assembly software based on long reads
By BioStar 2127 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...GMASS: a novel measure for genomeassembly structural similarity
By Abhimanyu Singh 2055 days agobioinfo.konkuk.ac.kr - The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo...CAR: Reconstructing Contiguous Regions of an Ancestral Genome
By Abhimanyu Singh 2751 days agowww.bx.psu.edu - We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1672 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly...
By Jit 1299 days agogithub.com - HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1084 days agoGenome assembly pipeline !Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 970 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 450 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...Research Associate Bioinformatics in IISc Recruitment 2020
Research Associate Bioinformatics in IISc Recruitment 2020 Essential Qualifications: Ph.D. (Bioinformatics/ Biophysics/ Biotechnology or any other stream of biological/ physical sciences) with a minimum of two publications in reputed peer...
