Jit
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GFinisher: a new strategy to refine and finish bacterial genome assemblies
By Jit 2782 days agogfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2669 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 2381 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPLiftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2076 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 1389 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...Genomic Scientist at UDSC
Centre for Genetic Manipulation of Crop Plants Department of Genetics University of Delhi South Campus NEW DELHI – 110 021 WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT & LAB / FIELD ATTENDANT 1 Research...Genomic Open-source Breeding informatics initiative
By BioStar 1886 days agocbsugobii05.biohpc.cornell.edu - To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs. To transform breeding by connecting diverse data with precision...kraken: A universal genomic coordinate translator for comparative genomics
By Jit 3013 days agogithub.com - If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomicsTACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest...
By Poonam Mahapatra 2854 days agowww.cebitec.uni-bielefeld.de - TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a...S-plot2: creates an interactive, two-dimensional heatmap of sequences
By Jit 2718 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...
