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ID:39205405
大小:198.58 KB
页数:5页
时间:2019-06-27
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1、TMSOLiDSystemApplicationDocumentation:csfasta_quality_filter.pl1Program1.1ProgramNameProgramNameProgramNamecsfasta_quality_filter.pl1.2ProgramVersionProgramVersionProgramVersioncsfasta_quality_filter.plv12Description2.1ApplicationApplicationApplicationQualityfilter
2、ingandtrimmingofSOLiD™colorspacereadspriortomultipleapplications.2.2DescriptionDescriptionDescriptionThisscripttakesacsfastafileandaQVfilefromaSOLiD™runandfiltersortrimsthereadsusingavarietyofuserselectedmethods.Outputisacsfastafileinwhichreadshavebeenfilteredortri
3、mmed,dependingonrunparameters.2.3ReleaseNotesReleaseNotesReleaseNotesFirstrelease.2.4Algorithm/ScriptDescriptionAlgorithm/ScriptDescriptionAlgorithm/ScriptDescriptionReadscanbefilteredortrimmedusingavarietyofmethodsincluding:•Trimmingofafixednumberofcolors•Trimming
4、afterarunofconsecutivelow-qualitycolors•Trimmingterminallow-qualitycolors•Removalofreadswithlowmedianqualityvalue•Removalofreadswithtoomanylow-qualitycolors•Removalofreadswithtoomanylowqualitycolorsinthefirsttencalls•Removalofreadsbelowaminimumreadlengthaftertrimmi
5、ngFurtherdetailsareintheUsageParameterssectionbelow.3Installation3.1InstallationInstructionsInstallationInstructionsInstallationInstructionsSimplydownloadthescriptandmakeitexecutable.YoumayneedtochangethefirstlineofthescriptifyourPerlisinanon-standardlocation(i.e.,
6、not/usr/bin/perl).YoumayneedtoinstalltheGetopt::LongPerlmodulefromCPAN.APPLIEDBIOSYSTEMSPAGE14Usage4.1UsageParametersUsageParametersUsageParameters----requiredrequiredrequiredrequired$csfasta_quality_filter.pl[options]-f-q-ocsfas
7、ta_file,qv_file,andoutput_filearefullpathsandfilenamesofthetwoinputfilesandtheoutputfile.4.2UsageParametersUsageParameters-UsageParameters---optionaloptionaloptionaloptionalShortValueValueDefaultnameLongnametyperangevalueDescription-m--min_median_qvint>01Readswithm
8、edianQVbelowthisvaluewillberemovedfromthedataset-l--min_read_lengthint>01Readsshorterthanthisvalueaftertrimmingwillberemovedfromthedataset-x--num
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