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AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome...
By Jit 1801 days agogithub.com - We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1084 days agoGenome assembly pipeline !Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 1003 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...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...RATT
By Jitendra Narayan 3216 days agoratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...NCBI Prokaryotic Genome Annotation Pipeline
By Jit 2752 days agowww.ncbi.nlm.nih.gov - NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2390 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
By LEGE 281 days agogithub.com - What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs...NanoPack: visualizing and processing long-read sequencing data
By Jit 2301 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1007 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...
