Bio.Sequencing package
Subpackages
- Bio.Sequencing.Applications package
- Module contents
BwaIndexCommandlineBwaAlignCommandlineBwaAlignCommandline.__init__()BwaAlignCommandline.BBwaAlignCommandline.EBwaAlignCommandline.IBwaAlignCommandline.MBwaAlignCommandline.NBwaAlignCommandline.OBwaAlignCommandline.RBwaAlignCommandline.__annotations__BwaAlignCommandline.__firstlineno__BwaAlignCommandline.__static_attributes__BwaAlignCommandline.bBwaAlignCommandline.b1BwaAlignCommandline.b2BwaAlignCommandline.cBwaAlignCommandline.dBwaAlignCommandline.eBwaAlignCommandline.iBwaAlignCommandline.kBwaAlignCommandline.lBwaAlignCommandline.nBwaAlignCommandline.oBwaAlignCommandline.qBwaAlignCommandline.read_fileBwaAlignCommandline.referenceBwaAlignCommandline.t
BwaSamseCommandlineBwaSampeCommandlineBwaSampeCommandline.__init__()BwaSampeCommandline.NBwaSampeCommandline.__annotations__BwaSampeCommandline.__firstlineno__BwaSampeCommandline.__static_attributes__BwaSampeCommandline.aBwaSampeCommandline.nBwaSampeCommandline.oBwaSampeCommandline.rBwaSampeCommandline.read_file1BwaSampeCommandline.read_file2BwaSampeCommandline.referenceBwaSampeCommandline.sai_file1BwaSampeCommandline.sai_file2
BwaBwaswCommandlineBwaBwaswCommandline.__init__()BwaBwaswCommandline.NBwaBwaswCommandline.TBwaBwaswCommandline.__annotations__BwaBwaswCommandline.__firstlineno__BwaBwaswCommandline.__static_attributes__BwaBwaswCommandline.aBwaBwaswCommandline.bBwaBwaswCommandline.cBwaBwaswCommandline.mate_fileBwaBwaswCommandline.qBwaBwaswCommandline.rBwaBwaswCommandline.read_fileBwaBwaswCommandline.referenceBwaBwaswCommandline.sBwaBwaswCommandline.tBwaBwaswCommandline.wBwaBwaswCommandline.z
BwaMemCommandlineBwaMemCommandline.__init__()BwaMemCommandline.ABwaMemCommandline.BBwaMemCommandline.CBwaMemCommandline.EBwaMemCommandline.HBwaMemCommandline.LBwaMemCommandline.MBwaMemCommandline.OBwaMemCommandline.PBwaMemCommandline.RBwaMemCommandline.TBwaMemCommandline.UBwaMemCommandline.__annotations__BwaMemCommandline.__firstlineno__BwaMemCommandline.__static_attributes__BwaMemCommandline.aBwaMemCommandline.cBwaMemCommandline.dBwaMemCommandline.kBwaMemCommandline.pBwaMemCommandline.rBwaMemCommandline.read_file1BwaMemCommandline.read_file2BwaMemCommandline.referenceBwaMemCommandline.tBwaMemCommandline.vBwaMemCommandline.w
NovoalignCommandlineNovoalignCommandline.__init__()NovoalignCommandline.__annotations__NovoalignCommandline.__firstlineno__NovoalignCommandline.__static_attributes__NovoalignCommandline.adapter3NovoalignCommandline.adapter5NovoalignCommandline.coresNovoalignCommandline.databaseNovoalignCommandline.formatNovoalignCommandline.fragmentNovoalignCommandline.gap_extendNovoalignCommandline.gap_openNovoalignCommandline.good_basesNovoalignCommandline.homopolymerNovoalignCommandline.miRNANovoalignCommandline.qual_digitsNovoalignCommandline.qualityNovoalignCommandline.r_methodNovoalignCommandline.read_calNovoalignCommandline.readfileNovoalignCommandline.recordedNovoalignCommandline.repeatsNovoalignCommandline.reportNovoalignCommandline.thresholdNovoalignCommandline.trimmingNovoalignCommandline.truncateNovoalignCommandline.unconvertedNovoalignCommandline.variationNovoalignCommandline.write_cal
SamtoolsViewCommandlineSamtoolsViewCommandline.__init__()SamtoolsViewCommandline.FSamtoolsViewCommandline.HSamtoolsViewCommandline.RSamtoolsViewCommandline.SSamtoolsViewCommandline.__annotations__SamtoolsViewCommandline.__firstlineno__SamtoolsViewCommandline.__static_attributes__SamtoolsViewCommandline.bSamtoolsViewCommandline.cSamtoolsViewCommandline.fSamtoolsViewCommandline.fast_bamSamtoolsViewCommandline.hSamtoolsViewCommandline.input_fileSamtoolsViewCommandline.lSamtoolsViewCommandline.oSamtoolsViewCommandline.qSamtoolsViewCommandline.rSamtoolsViewCommandline.regionSamtoolsViewCommandline.tSamtoolsViewCommandline.u
SamtoolsCalmdCommandlineSamtoolsCalmdCommandline.__init__()SamtoolsCalmdCommandline.ASamtoolsCalmdCommandline.CSamtoolsCalmdCommandline.ESamtoolsCalmdCommandline.SSamtoolsCalmdCommandline.__annotations__SamtoolsCalmdCommandline.__firstlineno__SamtoolsCalmdCommandline.__static_attributes__SamtoolsCalmdCommandline.bSamtoolsCalmdCommandline.eSamtoolsCalmdCommandline.input_bamSamtoolsCalmdCommandline.rSamtoolsCalmdCommandline.refSamtoolsCalmdCommandline.u
SamtoolsCatCommandlineSamtoolsFaidxCommandlineSamtoolsFixmateCommandlineSamtoolsIdxstatsCommandlineSamtoolsIndexCommandlineSamtoolsMergeCommandlineSamtoolsMergeCommandline.__init__()SamtoolsMergeCommandline.RSamtoolsMergeCommandline.__annotations__SamtoolsMergeCommandline.__firstlineno__SamtoolsMergeCommandline.__static_attributes__SamtoolsMergeCommandline.bamSamtoolsMergeCommandline.fSamtoolsMergeCommandline.fast_bamSamtoolsMergeCommandline.hSamtoolsMergeCommandline.nSamtoolsMergeCommandline.outputSamtoolsMergeCommandline.rSamtoolsMergeCommandline.u
SamtoolsMpileupCommandlineSamtoolsMpileupCommandline.__init__()SamtoolsMpileupCommandline.ASamtoolsMpileupCommandline.BSamtoolsMpileupCommandline.CSamtoolsMpileupCommandline.DSamtoolsMpileupCommandline.ESamtoolsMpileupCommandline.ISamtoolsMpileupCommandline.LSamtoolsMpileupCommandline.MSamtoolsMpileupCommandline.QSamtoolsMpileupCommandline.SSamtoolsMpileupCommandline.__annotations__SamtoolsMpileupCommandline.__firstlineno__SamtoolsMpileupCommandline.__static_attributes__SamtoolsMpileupCommandline.bSamtoolsMpileupCommandline.dSamtoolsMpileupCommandline.eSamtoolsMpileupCommandline.fSamtoolsMpileupCommandline.gSamtoolsMpileupCommandline.hSamtoolsMpileupCommandline.illumina_13SamtoolsMpileupCommandline.input_fileSamtoolsMpileupCommandline.lSamtoolsMpileupCommandline.oSamtoolsMpileupCommandline.pSamtoolsMpileupCommandline.qSamtoolsMpileupCommandline.rSamtoolsMpileupCommandline.u
SamtoolsPhaseCommandlineSamtoolsPhaseCommandline.__init__()SamtoolsPhaseCommandline.ASamtoolsPhaseCommandline.FSamtoolsPhaseCommandline.QSamtoolsPhaseCommandline.__annotations__SamtoolsPhaseCommandline.__firstlineno__SamtoolsPhaseCommandline.__static_attributes__SamtoolsPhaseCommandline.bSamtoolsPhaseCommandline.in_bamSamtoolsPhaseCommandline.kSamtoolsPhaseCommandline.q
SamtoolsReheaderCommandlineSamtoolsRmdupCommandlineSamtoolsSortCommandlineSamtoolsVersion0xSortCommandlineSamtoolsVersion0xSortCommandline.__init__()SamtoolsVersion0xSortCommandline.__annotations__SamtoolsVersion0xSortCommandline.__firstlineno__SamtoolsVersion0xSortCommandline.__static_attributes__SamtoolsVersion0xSortCommandline.inputSamtoolsVersion0xSortCommandline.mSamtoolsVersion0xSortCommandline.nSamtoolsVersion0xSortCommandline.oSamtoolsVersion0xSortCommandline.out_prefix
SamtoolsVersion1xSortCommandlineSamtoolsVersion1xSortCommandline.__init__()SamtoolsVersion1xSortCommandline.ISamtoolsVersion1xSortCommandline.OSamtoolsVersion1xSortCommandline.TSamtoolsVersion1xSortCommandline.__annotations__SamtoolsVersion1xSortCommandline.__firstlineno__SamtoolsVersion1xSortCommandline.__static_attributes__SamtoolsVersion1xSortCommandline.inputSamtoolsVersion1xSortCommandline.mSamtoolsVersion1xSortCommandline.nSamtoolsVersion1xSortCommandline.o
SamtoolsTargetcutCommandlineSamtoolsTargetcutCommandline.__init__()SamtoolsTargetcutCommandline.QSamtoolsTargetcutCommandline.__annotations__SamtoolsTargetcutCommandline.__firstlineno__SamtoolsTargetcutCommandline.__static_attributes__SamtoolsTargetcutCommandline.em0SamtoolsTargetcutCommandline.em1SamtoolsTargetcutCommandline.em2SamtoolsTargetcutCommandline.fSamtoolsTargetcutCommandline.iSamtoolsTargetcutCommandline.in_bam
- Module contents
Submodules
Module contents
Code to deal with various programs for sequencing and assembly.
This code deals with programs such as Phred, Phrap and Consed – which provide utilities for calling bases from sequencing reads, and assembling sequences into contigs.