Jit
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Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2534 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...Ranbow: a haplotype assembler for polyploid genomes
By Jit 2378 days agowww.molgen.mpg.de - Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing,...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1678 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...odgi: optimized dynamic genome/graph implementation
By Abhimanyu Singh 1037 days agogithub.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 1010 days agowww.genomicus.bio.ens.psl.eu - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
By Abhimanyu Singh 2224 days agoancestralgenomes.org - Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...KisSplice
By Jit 3032 days agokissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2238 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 1922 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPcoursera genome assembly tutorial
By Jit 2566 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)
