3952 days ago
3952 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...thms for de novo short read assembly using de Bruijn graphs. Zerbino & Birney, Genom...549-556, 2012 Full Text [Describes the String Graph Assembler (SGA), which assemb...site UK RAD Sequencing Wiki page, with bibliography and RADTools software downlo...3785 days ago
List of bioinformatics open source projects/software.
Open source software is software that can be freely used, changed, and shared (in mod...prototyping Bio4j http://bio4j.com/ Bio4j is a bioinformatics platform and graph based database built around m...3763 days ago
Commercial and public next-gen-seq (NGS) software
...gh quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities,...Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach. MIRA2 - MIRA (Mimic...3525 days ago
Software packages for next gen sequence analysis
...gh quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities,...Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach. * MIRA2 - MIRA (Mim...3249 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...2Kplus2 Description: algorithm searches graphs produced by de novo assembler...le nucleotide polymorphisms in transformed De Bruijn graphs using Cortex assembler.&rdqu...ut: FASTA Output: html or plain text format, graphical display of results E...2915 days ago
Genome Assembly Tools and Software - PART1 !!
...protein-coding genes using a graph structure combining both de Bruijn graphs and protein HMMs. The...ntend of using traditional de Bruijn Graph, SWAP-Assembler adopts multi-step bi-directed graph (MSG). With MSG, the standard...mics Assembly via Succinct de Bruijn graph MEGAHIT is a single node a...2692 days ago
Awesome perl frameworks, libraries and software - PART 1
A curated list of awesome Perl frameworks, l...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...2495 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...ic mutations; algorithm uses k-mers and is based on colored de Bruijn graphs) Software (Python) http://g...sequences and the distances between them based on assembly using de Bruijn graphs and Bray–Curtis dissim...2377 days ago