ABIF-File-Format

1ABIFFileFormatSpecificationandSampleFileSchemaAppliedBiosystemsGeneticAnalysisDataFileFormatSeptember2009SUBJECT:ABIFFileFormatSpecificationandSampleFileSchemaInthisdocumentThisdocumentincludesthefollowingtopics:Introduction........................................................2Anoteaboutsupport.................................................2Importantnotesaboutcompatibility.....................................3TheABIFfileformat................................................4OverviewoftheABIFformat..........................................5DetailedstructureoftheABIFfile......................................7Header............................................................7Directory.........................................................10Datatypes........................................................13Notesonusingthe'user'datatype.....................................19Samplefileschemas................................................20ABIPRISM3100and3100-AvantGeneticAnalyzertags...................21AppliedBiosystems3130/3130xlGeneticAnalyzertags....................27AppliedBiosystems3500/3500xlGeneticAnalyzertags....................33AppliedBiosystems3730/3730xlDNAAnalyzertags......................442AppliedBiosystemsGeneticAnalysisDataFileFormatABIFFileFormatSpecificationandSampleFileSchemaIntroductionThisdocumentisintendedforprogrammersorbioinformaticsgroupswhowishtoperformadditionalanalysisorothermanipulationofab1and/orfsafiles.Theab1fileisafiletypeproducedbyDataCollectionsoftwaregeneratingsequencingdata,withtheextension.ab1.ThefsafileisafiletypeproducedbyDataCollectionsoftwaregeneratingfragmentanalysisdata,withtheextension.fsa.Boththeab1andfsafilesusetheABIFfileformat.TheABIFfileformatspecifiesthegeneralrulesonhowthefileisconstructed,andthereforetherulesonhowitcanberead.Elementsofdatastoredinthefileareassociatedwithtags,whichareanalogoustothekeysina(key,value)mapping.TheABIFfileformatbyitselfdoesnotspecifytheschemafortheab1andfsafiles,i.e.whichtagsarewrittenandwhen.Theseschemaarespecifictotheinstrumentandsoftwareversionwhichcreatedthefile.ThisuserbulletindescribestheABIFformat.FollowingtheABIFspecificationaretheschemasforeachinstrument-softwarecombination,forboththeab1andfsafilesstartingonpage21.Schemas(tableswiththevalidtags)forthefollowinginstrumentsaregiven:•ABIPRISM®3100and3100-Avant™GeneticAnalyzertags(page21)�AppliedBiosystems3130/3130xlGeneticAnalyzertags(page27)�AppliedBiosystems3500/3500xlGeneticAnalyzertags(page33)�AppliedBiosystems3730/3730xlDNAAnalyzertags(page44)AnoteaboutsupportIMPORTANT!AppliedBiosystemsdoesnotsupportusersofthisspecificationinanyway.Pleasedonotcalltechnicalsupportforaddditonalinformationpertainingtothisspecification.3ImportantnotesaboutcompatibilityABIFFileFormatSpecificationandSampleFileSchemaImportantnotesaboutcompatibilityBackwardandcrosscompatibilitySometagsexistintheab1andfsafilesforbackwardcompatibilitywithearlierversionsofAppliedBiosystemssoftware.Theyarenolongerusedbycurrentversionsofdownstreamanalysisapplications.Theab1andfsaschemadocumentationisprovidedforaspecificinstrumentmodelandsoftwareversion.Thereisnoguaranteethatthetaggeddatadescribedwillbeconsistentwithfilesproducedbyearliersoftwarereleasesand/orotherinstrumentmodels.ForwardcompatibilityThecriticaldataintheab1andfsafilesisstable,andingeneralnewdatawillextendtheexistingschema.However,AppliedBiosystemsprovidesnoguaranteethatalltaggeddataelementswillbepresent,consistent,orsupportedinfutureversionsofthesoftware,particularlyfordatathatpertainstothedetailsofinstrumentcontrolorsoftwareintegration.CompatibilityofeditedsamplefilesTherearetwowaystomodifysamplefiles(ab1andfsafiles),eitherbyaddingnewtagsorchangingexistingtags.SamplefileswithnewtagsaddedbyauserfollowingAppliedBiosystems'instructionsassetforthinDetailedstructureoftheABIFfileonpage7,shouldcontinuetobecompatiblewithAppliedBiosystemssoftware.AnymodificationtosamplefilesbychangingtheexistingtagsmayresultinthefilenolongerbeingcompatiblewithAppliedBiosystemssoftware.IMPORTANT!AppliedBiosystemsdoesnotrecommendanymodificationofthesoftwarefiles.AppliedBiosystemsdoesnotsupporttheeditingofsamplefilesinanywayandmakesnoguaranteesastothecompatibilityofsuchfileswithAppliedBiosystemssoftware.4AppliedBiosystemsGeneticAnalysisDataFileFormatABIFFileFormatSpecificationandSampleFileSchemaTheABIFfileformatIntroductionTheABIFfileformatisabinaryfileformatforstoringdata.Elementsofdatastoredinthefileareassociatedwithtags,whichareanalogoustothekeysina(key,value)mapping.TheABIFformatcanaccommodateamoderatenumber(1000)ofheterogeneousdataitems.Adataitemcanbeascalarvalueoranarray.Thebasicdatatypesare8,16,and32bitintegers,32bitfloating-pointvalues,andASCIIcharacters.Therearealsotwocompounddatatypes:dateandtime.Thedatatypeofeachitemisidentifiedbyanelementtypecode.Eachdataitemisuniquelyidentified(tagged)withinafilebyatagnameandatagnumber.Thetagnameandtagnumberarestoredinternallyas32-bitintegers;thetagnameisintendedtobedefinedasastringoffour8-bitASCIIcharactersstoredinbig-endi