sc932.github.io - Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and...
github.com - HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler...
www.ncbi.nlm.nih.gov - The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny,...
elp.ucdavis.edu - Generic Genome Browser Version 2: A Tutorial for Administrators
This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD,...
abims.sb-roscoff.fr - Function
WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common...
R Graphical Cookbook by Winston Chang
A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown...
bitbucket.org - RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It...
github.com - v0.0 by Glenn Hickey (hickey@soe.ucsc.edu)
Progressive Cactus is a whole-genome alignment package.
Requirements
git
gcc 4.2 or newer
python 2.7
wget
64bit processor and build environment
150GB+ of memory on at least one machine when...
www.sequenceontology.org - We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers...