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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of...
By Jit 2300 days agocatchenlab.life.illinois.edu - Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to...CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
By Jit 2209 days agogithub.com - Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2114 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 2017 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 1478 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...CGView.js is a Circular Genome Viewing tool
By LEGE 800 days agohttps://js.cgview.ca/ - CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView. CGView.js is the genome viewer of Proksee, an expert system for genome...NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic...
By LEGE 633 days agogithub.com - NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of...Bourque Lab
The goal of the lab is to understand mammalian genomes using comparative genomic and epigenomic analyses. Areas of interest include: the evolution of regulatory sequences, the role of transposable elements in gene regulation and the impact of genome...Papenfuss Lab
The human genome project and similar projects in disease-causing organisms such as Plasmodium falciparum, which causes malaria in humans, have provided new tools for discovery in biology and have accelerated the development of understanding in human...Bioinformatics PhD studentship available in New Zealand
Bioinformatics PhD studentship available in New Zealand The importance of transcriptional control has been explored in a burgeoning line of research over several decades; nevertheless, we are still far from having a complete picture of the...
