Toward almost closed genomes with GapFiller 英文参考文献.docVIP

BoetzerandPirovanoGenomeBiology2012,13:R56 /2012/13/6/R56 SOFTWARE OpenAccess TowardalmostclosedgenomeswithGapFiller MartenBoetzerandWalterPirovano* Abstract Denovoassemblyisacommonlyusedapplicationofnext-generationsequencingexperiments.Theultimategoal istopuzzlemillionsofreadsintoonecompletegenome,althoughdraftassembliesusuallyresultinanumberof gappedscaffoldsequences.Inthispaperweproposeanautomatedstrategy,calledGapFiller,toreliablyclosegaps withinscaffoldsusingpairedreads.Themethodshowsgoodresultsonbothbacterialandeukaryoticdatasets, allowingonlyfewerrors.Asaconsequence,theamountofadditionalwetlabworkneededtocloseagenomeis drasticallyreduced.Thesoftwareisavailableat/bioinformatics-tools/. Background aconsequence, atpresent,mostgenomeassemblies are Denovosequencingofunknownspeciesandvariantshas still incomplete after scaffolding and would ideally becomeamajorapplication ofnext-generation sequen- requireaccurategapclosure.Giventhatmanualclosure cing (NGS) technologies. Asaconsequence, there isa ofincompleteregionswithSangersequencingisexpen- highdemandfordenovoassemblytoolsthatcanrecon- sive,genomeassembliessubmittedtosequencedatabases struct the genomic sequence from millions of short oftenlackasignificantnumberofnucleotides,especially reads. Atpresent avast number oftools isavailable to inthecaseoflargereukaryotes.Importantly,themissing createadraftassemblythatrepresents thegenomeina repetitiveorlow-coverageregionsmaycontainessential numberofcontiguoussequences(contigs),suchasVelvet functionsfortheorganismstudied. [1], ABySS [2], andSOAPdenovo [3]. Nonetheless, the Inthis study weaim toreduce the number ofunde- fullclosureofacompletegenomeremainsachallenging finednucleotides byautomatically filling inthegapped andoftenexpensive task.Generally, problems reside in regions within scaffolds. Forthispurpose, paired reads the assembly oflow-coverage areas andrepetitive ele- are(re)used.Inbrief,ourGapFillermethodseekstofind ments.