3945 days ago
3945 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next generation quant...o short read assembly using de Bruijn graphs. Zerbino & Birney, Genom...2012 Full Text [Describes the String Graph Assembler (SGA), which assemb...RAD Sequencing Wiki page, with bibliography and RADTools software downlo...3778 days ago
List of bioinformatics open source projects/software.
Open source software is software that can be freely used, changed, and shared (in modi...prototyping Bio4j http://bio4j.com/ Bio4j is a bioinformatics platform and graph based database built around m...3756 days ago
List of In-silico Binding Site Prediction Tools
...Computed Atlas of Surface Topography of proteins (CASTp) provides a...of proteins. CASTp includes a graphical user interface, flexible in...icted pocket had at-least 10% overlap with the actual ligand. The...program for the detection and graphical analysis of protein surfa...3743 days ago
Next generation sequencing in R or bioconductor environment
...SIPeS RNA-Seq Analysis Counting Reads that Overlap with Annotation Ranges ...ting provided by this infrastructure are countOverlaps and summarizeOverlaps. For t...nates HilbertVis: Hilbert genome plots GenomeGraphs: Plotting genomic informatio...3624 days ago
Commercial and public next-gen-seq (NGS) software
...rom short reads. Assemblies are presented in a graph form that retains ambiguities,...me Analyzer. Edena is based on the traditional overlap layout paradigm. By D. Hern...ublished in Genome Research). Uses a de Bruijn graph approach. MIRA2 - MIRA (Mimic...3518 days ago
Software packages for next gen sequence analysis
...rom short reads. Assemblies are presented in a graph form that retains ambiguities,...me Analyzer. Edena is based on the traditional overlap layout paradigm. By D. Hern...ublished in Genome Research). Uses a de Bruijn graph approach. * MIRA2 - MIRA (Mim...3242 days ago
Genome Assembly Tools and Software - PART1 !!
...ories: string-based model and graph-based model. We therefore list...protein-coding genes using a graph structure combining both de Bru...adopts multi-step bi-directed graph (MSG). With MSG, the standard g...ene assembly, homology-guided overlap graph construction, and careful gra...2685 days ago
Awesome perl frameworks, libraries and software - PART 1
A curated list of awesome Perl frameworks, li...itoring MySQL servers rizen/Facebook-Graph - A perl module to help...igate the intricacies of the Facebook Graph API. lhost/sendxmpp - p...tg - MRTG - Multi Router Traffic Grapher monitoring-plugins/monitor...2488 days ago