ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and...scaffolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes...2023 days ago
Genome Annotation using MAKER tutorial !
MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predict...hing. Here I will describe a de novo genome annotation for Boa const...is easy to use this as a guide to annotate any genome.2023 days ago
Versatile genome assembly evaluation with QUAST-LG
QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in...on the assembly completeness and contiguity for a given genome...2022 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modifi...on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-...2016 days ago
2013 days ago
Hawkeye: an interactive visual analytics tool for genome assemblies
Genome sequencing remains an inexact science, and genome sequences can contain significan...ur new visual analytics tool for genome assemblies, designed to aid i...as part of the open source AMOS project http://amos.sourceforge.net/hawkeye. https://genomebiology.biomedcentral.com/artic...2011 days ago
GenoViz: Visualization software for genomics
...ur flagship product is Integrated Genome Browser (IGB).For more inform...://bioviz.org.Source code for the project was hosted here for many yea...tbucket.org/lorainelab/integrated-genome-browser. We are still using So...eel free to get in touch. Contact project head Ann Loraine (aloraine@un...2010 days ago
GenomeView: genome browser and annotation editor
GenomeView is a genome browser and annotation editor that displays reference sequenc...ts are supported. Local and internet files can be loaded.This project has moved to GitHub: https://github.com/GenomeView/genomeview2010 days ago
2010 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
...or the investigation of CNVs in largescale projects, as well as in clinical res...y available at http://sourceforge.net/projects/excavatortool/.EXCAVATOR is...ncing data.EXCAVATOR has been published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abs...2008 days ago