HiGlass: a tool for exploring genomic contact matrices and tracks.
HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a l...thin a Docker container. The HiC data in the examples below is from Rao et al. (2014) http://higlass.io/2171 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro...on for de novo genome assembly via transposase contiguity. Genome Research 2014 Dec;24(12):2041-9. doi: ...2199 days ago
GenoViz: Visualization software for genomics
GenoViz provides software applications and re-usable components for data visualizati...ttp://bioviz.org.Source code for the project was hosted here for many years. In 2014, we moved to a new git reposi...1966 days ago
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Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan geno...1946 days ago
DISTRUCT: a program for the graphical display of population structure
distruct is a program that can be used to graphically display results produced...nd comments or problems with distruct to Noah Rosenberg. October 15, 2014 — Users of Distruct may...1884 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
SHAMAN is a shiny application for differential analysis o...undant features as suggested in [McMurdie and Holmes 2014] and [Jonsson2016]. SHAMAN ro...Generalized Linear Model implemented in DESeq2 [Love 2014].SHAMAN is compatible with st...1373 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in...ually good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 201...1059 days ago