Qualimap: evaluating next-generation sequencing alignment data
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...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) Jg. 28; H. 20; S. 2678 - 2679 |
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| Hauptverfasser: | , , , , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
Oxford
Oxford University Press
15.10.2012
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| ISSN: | 1367-4803, 1367-4811, 1367-4811 |
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| 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. |
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| AbstractList | 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. 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.MOTIVATIONThe 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.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.RESULTSWe 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.Qualimap is freely available from http://www.qualimap.org.AVAILABILITYQualimap is freely available from http://www.qualimap.org. 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. 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. Qualimap is freely available from http://www.qualimap.org. |
| Author | Tarazona, Sonia Conesa, Ana Okonechnikov, Konstantin Carbonell, José Götz, Stefan Cruz, Luis M. Dopazo, Joaquín García-Alcalde, Fernando Meyer, Thomas F. |
| Author_xml | – sequence: 1 givenname: Fernando surname: García-Alcalde fullname: García-Alcalde, Fernando – sequence: 2 givenname: Konstantin surname: Okonechnikov fullname: Okonechnikov, Konstantin – sequence: 3 givenname: José surname: Carbonell fullname: Carbonell, José – sequence: 4 givenname: Luis M. surname: Cruz fullname: Cruz, Luis M. – sequence: 5 givenname: Stefan surname: Götz fullname: Götz, Stefan – sequence: 6 givenname: Sonia surname: Tarazona fullname: Tarazona, Sonia – sequence: 7 givenname: Joaquín surname: Dopazo fullname: Dopazo, Joaquín – sequence: 8 givenname: Thomas F. surname: Meyer fullname: Meyer, Thomas F. – sequence: 9 givenname: Ana surname: Conesa fullname: Conesa, Ana |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26451035$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/22914218$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1038/nmeth.1376 10.1186/gb-2009-10-3-r32 10.1038/nrg2626 10.1093/bioinformatics/btq614 10.1186/gb-2009-10-3-r25 10.1038/nbt0509-455 10.1093/bioinformatics/btp352 10.1093/bioinformatics/btq247 10.1093/bioinformatics/bts196 10.1101/gr.079558.108 10.1093/nar/gkq1064 10.1093/bioinformatics/btp120 |
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| References | Harismendy (2023012513140612300_bts503-B4) 2009; 10 Langmead (2023012513140612300_bts503-B5) 2009; 10 Li (2023012513140612300_bts503-B7) 2009; 25 Flicek (2023012513140612300_bts503-B2) 2009; 6 Trapnell (2023012513140612300_bts503-B12) 2009; 25 Lassmann (2023012513140612300_bts503-B6) 2011; 27 Marioni (2023012513140612300_bts503-B8) 2008; 18 Statham (2023012513140612300_bts503-B10) 2010; 26 DeLuca (2023012513140612300_bts503-B1) 2012; 28 Flicek (2023012513140612300_bts503-B3) 2011; 39 Trapnell (2023012513140612300_bts503-B11) 2009; 27 Metzker (2023012513140612300_bts503-B9) 2009; 11 |
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| Snippet | Motivation: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide... The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments... |
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| SubjectTerms | Algorithms Biological and medical sciences Fundamental and applied biological sciences. Psychology General aspects Genomics High-Throughput Nucleotide Sequencing Humans Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Quality Control Sequence Alignment - standards Software |
| Title | Qualimap: evaluating next-generation sequencing alignment data |
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