Bioinformatics for next generation sequencing data.
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.
Diagnostic Genetic Unit, Careggi Hospital, Azienda Ospedaliera Universitaria Careggi, University of Florence, Florence, Italy. albertomagi@gmail.com.
Alberto
A
Magi
Diagnostic Genetic Unit, Careggi Hospital, Azienda Ospedaliera Universitaria Careggi, University of Florence, Florence, Italy. matteo.benelli@gmail.com.
Matteo
M
Benelli
Diagnostic Genetic Unit, Careggi Hospital, Azienda Ospedaliera Universitaria Careggi, University of Florence, Florence, Italy. gozzinial@aou-careggi.toscana.it.
Alessia
A
Gozzini
Diagnostic Genetic Unit, Careggi Hospital, Azienda Ospedaliera Universitaria Careggi, University of Florence, Florence, Italy. girolamif@aou-careggi.toscana.it.
Francesca
F
Girolami
Diagnostic Genetic Unit, Careggi Hospital, Azienda Ospedaliera Universitaria Careggi, University of Florence, Florence, Italy. torricellif@aou-careggi.toscana.it.
Francesca
F
Torricelli
Department of Internal Medicine, University of Florence Medical School, Florence, Italy. m.brandi@dmi.unifi.it.
Maria Luisa
ML
Brandi