Bio.Sequencing package
Subpackages
- Bio.Sequencing.Applications package
- Module contents
BwaIndexCommandline
BwaAlignCommandline
BwaAlignCommandline.__init__()
BwaAlignCommandline.B
BwaAlignCommandline.E
BwaAlignCommandline.I
BwaAlignCommandline.M
BwaAlignCommandline.N
BwaAlignCommandline.O
BwaAlignCommandline.R
BwaAlignCommandline.b
BwaAlignCommandline.b1
BwaAlignCommandline.b2
BwaAlignCommandline.c
BwaAlignCommandline.d
BwaAlignCommandline.e
BwaAlignCommandline.i
BwaAlignCommandline.k
BwaAlignCommandline.l
BwaAlignCommandline.n
BwaAlignCommandline.o
BwaAlignCommandline.q
BwaAlignCommandline.read_file
BwaAlignCommandline.reference
BwaAlignCommandline.t
BwaSamseCommandline
BwaSampeCommandline
BwaBwaswCommandline
BwaBwaswCommandline.__init__()
BwaBwaswCommandline.N
BwaBwaswCommandline.T
BwaBwaswCommandline.a
BwaBwaswCommandline.b
BwaBwaswCommandline.c
BwaBwaswCommandline.mate_file
BwaBwaswCommandline.q
BwaBwaswCommandline.r
BwaBwaswCommandline.read_file
BwaBwaswCommandline.reference
BwaBwaswCommandline.s
BwaBwaswCommandline.t
BwaBwaswCommandline.w
BwaBwaswCommandline.z
BwaMemCommandline
BwaMemCommandline.__init__()
BwaMemCommandline.A
BwaMemCommandline.B
BwaMemCommandline.C
BwaMemCommandline.E
BwaMemCommandline.H
BwaMemCommandline.L
BwaMemCommandline.M
BwaMemCommandline.O
BwaMemCommandline.P
BwaMemCommandline.R
BwaMemCommandline.T
BwaMemCommandline.U
BwaMemCommandline.a
BwaMemCommandline.c
BwaMemCommandline.d
BwaMemCommandline.k
BwaMemCommandline.p
BwaMemCommandline.r
BwaMemCommandline.read_file1
BwaMemCommandline.read_file2
BwaMemCommandline.reference
BwaMemCommandline.t
BwaMemCommandline.v
BwaMemCommandline.w
NovoalignCommandline
NovoalignCommandline.__init__()
NovoalignCommandline.adapter3
NovoalignCommandline.adapter5
NovoalignCommandline.cores
NovoalignCommandline.database
NovoalignCommandline.format
NovoalignCommandline.fragment
NovoalignCommandline.gap_extend
NovoalignCommandline.gap_open
NovoalignCommandline.good_bases
NovoalignCommandline.homopolymer
NovoalignCommandline.miRNA
NovoalignCommandline.qual_digits
NovoalignCommandline.quality
NovoalignCommandline.r_method
NovoalignCommandline.read_cal
NovoalignCommandline.readfile
NovoalignCommandline.recorded
NovoalignCommandline.repeats
NovoalignCommandline.report
NovoalignCommandline.threshold
NovoalignCommandline.trimming
NovoalignCommandline.truncate
NovoalignCommandline.unconverted
NovoalignCommandline.variation
NovoalignCommandline.write_cal
SamtoolsViewCommandline
SamtoolsViewCommandline.__init__()
SamtoolsViewCommandline.F
SamtoolsViewCommandline.H
SamtoolsViewCommandline.R
SamtoolsViewCommandline.S
SamtoolsViewCommandline.b
SamtoolsViewCommandline.c
SamtoolsViewCommandline.f
SamtoolsViewCommandline.fast_bam
SamtoolsViewCommandline.h
SamtoolsViewCommandline.input_file
SamtoolsViewCommandline.l
SamtoolsViewCommandline.o
SamtoolsViewCommandline.q
SamtoolsViewCommandline.r
SamtoolsViewCommandline.region
SamtoolsViewCommandline.t
SamtoolsViewCommandline.u
SamtoolsCalmdCommandline
SamtoolsCalmdCommandline.__init__()
SamtoolsCalmdCommandline.A
SamtoolsCalmdCommandline.C
SamtoolsCalmdCommandline.E
SamtoolsCalmdCommandline.S
SamtoolsCalmdCommandline.b
SamtoolsCalmdCommandline.e
SamtoolsCalmdCommandline.input_bam
SamtoolsCalmdCommandline.r
SamtoolsCalmdCommandline.ref
SamtoolsCalmdCommandline.u
SamtoolsCatCommandline
SamtoolsFaidxCommandline
SamtoolsFixmateCommandline
SamtoolsIdxstatsCommandline
SamtoolsIndexCommandline
SamtoolsMergeCommandline
SamtoolsMpileupCommandline
SamtoolsMpileupCommandline.__init__()
SamtoolsMpileupCommandline.A
SamtoolsMpileupCommandline.B
SamtoolsMpileupCommandline.C
SamtoolsMpileupCommandline.D
SamtoolsMpileupCommandline.E
SamtoolsMpileupCommandline.I
SamtoolsMpileupCommandline.L
SamtoolsMpileupCommandline.M
SamtoolsMpileupCommandline.Q
SamtoolsMpileupCommandline.S
SamtoolsMpileupCommandline.b
SamtoolsMpileupCommandline.d
SamtoolsMpileupCommandline.e
SamtoolsMpileupCommandline.f
SamtoolsMpileupCommandline.g
SamtoolsMpileupCommandline.h
SamtoolsMpileupCommandline.illumina_13
SamtoolsMpileupCommandline.input_file
SamtoolsMpileupCommandline.l
SamtoolsMpileupCommandline.o
SamtoolsMpileupCommandline.p
SamtoolsMpileupCommandline.q
SamtoolsMpileupCommandline.r
SamtoolsMpileupCommandline.u
SamtoolsPhaseCommandline
SamtoolsReheaderCommandline
SamtoolsRmdupCommandline
SamtoolsSortCommandline
SamtoolsVersion0xSortCommandline
SamtoolsVersion1xSortCommandline
SamtoolsTargetcutCommandline
- 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.