@article {938,
	title = {Qualimap: evaluating next-generation sequencing alignment data.},
	journal = {Bioinformatics (Oxford, England)},
	volume = {28},
	year = {2012},
	month = {2012 Oct 15},
	pages = {2678-9},
	abstract = {MOTIVATION: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate downstream analyses. RESULTS: We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses. AVAILABILITY: Qualimap is freely available from http://www.qualimap.org. CONTACT: aconesa@cipf.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
	keywords = {NGS},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/bts503},
	url = {http://bioinformatics.oxfordjournals.org/content/28/20/2678.long},
	author = {Garc{\'\i}a-Alcalde, Fernando and Okonechnikov, Konstantin and Carbonell, Jos{\'e} and Cruz, Luis M and G{\"o}tz, Stefan and Sonia Tarazona and Joaqu{\'\i}n Dopazo and Meyer, Thomas F and Ana Conesa}
}
@article {20361057,
	title = {Initial genomics of the human nucleolus.},
	journal = {PLoS genetics},
	volume = {6},
	year = {2010},
	month = {2010},
	pages = {e1000889},
	abstract = {<p>We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs) in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4\% of the genome. Bioinformatic evaluation showed that NAD-localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD-specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture.</p>},
	keywords = {NGS, nucleolus},
	doi = {10.1371/journal.pgen.1000889},
	url = {http://www.plosgenetics.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pgen.1000889},
	author = {N{\'e}meth, Attila and Ana Conesa and Santoyo-L{\'o}pez, Javier and Medina, Ignacio and Montaner, David and P{\'e}terfia, B{\'a}lint and Solovei, Irina and Cremer, Thomas and Dopazo, Joaquin and L{\"a}ngst, Gernot}
}
