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A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly
Genes 2010, 1(2), 294-307; doi:10.3390/genes1020294

Bioinformatics for Next Generation Sequencing Data

1,2,3,†,* , 1,2,4,†
1 Diagnostic Genetic Unit, Careggi Hospital, Azienda Ospedaliera Universitaria Careggi, University of Florence, Florence, Italy 2 Center for the Study of Complex Dynamics, University of Florence, Florence, Italy 3 Surgical Critical Care, University of Florence, Florence, Italy 4 INFN, Sezione di Firenze, Firenze, Italy 5 Department of Internal Medicine, University of Florence Medical School, Florence, Italy These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 27 July 2010 / Revised: 30 August 2010 / Accepted: 14 September 2010 / Published: 14 September 2010
(This article belongs to the Special Issue Next Generation DNA Sequencing)
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The emergence of next-generation sequencing (NGS) platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.
Keywords: sequencing; data analysis; bioinformatics sequencing; data analysis; bioinformatics
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Magi, A.; Benelli, M.; Gozzini, A.; Girolami, F.; Torricelli, F.; Brandi, M.L. Bioinformatics for Next Generation Sequencing Data. Genes 2010, 1, 294-307.

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