csfasta_quality_filter_documentation英文文献资料

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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