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.
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.
Authors: Patrick D Brophy; Maria Rasmussen; Mrutyunjaya Parida; Greg Bonde; Benjamin W Darbro; Xiaojing Hong; Jason C Clarke; Kevin A Peterson; James Denegre; Michael Schneider; Caroline R Sussman; Lone Sunde; Dorte L Lildballe; Jens Michael Hertz; Robert A Cornell; Stephen A Murray; J Robert Manak Journal: Genetics Date: 2017-07-24 Impact factor: 4.562
Authors: Inna Tabansky; Yupu Liang; Maya Frankfurt; Martin A Daniels; Matthew Harrigan; Sarah Stern; Teresa A Milner; Rebecca Leshan; Rrezarta Rama; Tabea Moll; Jeffrey M Friedman; Joel N H Stern; Donald W Pfaff Journal: Proc Natl Acad Sci U S A Date: 2018-07-02 Impact factor: 11.205
Authors: Casimiro Gerarduzzi; Ramya K Kumar; Priyanka Trivedi; Amrendra K Ajay; Ashwin Iyer; Sarah Boswell; John N Hutchinson; Sushrut S Waikar; Vishal S Vaidya Journal: JCI Insight Date: 2017-04-20
Authors: R Rebecca Love; Aaron M Steele; Mamadou B Coulibaly; Sékou F Traore; Scott J Emrich; Michael C Fontaine; Nora J Besansky Journal: Mol Ecol Date: 2016-11-09 Impact factor: 6.185
Authors: Brendan R E Ansell; Malcolm J McConville; Louise Baker; Pasi K Korhonen; Samantha J Emery; Staffan G Svärd; Robin B Gasser; Aaron R Jex Journal: Antimicrob Agents Chemother Date: 2016-09-23 Impact factor: 5.191