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Pacbio RS II 一级分析工具

Pacbio RS II Primary Analysis Tools, used for generate .bax.h5 files from .trc.h5 files on instrument.

Pacbio RS II测序仪一级分析软件,从测序仪中提取,经测试可用。可将测序原始.trc.h5转换成bax.h5文件,暂未公开使用文档,

具体使用方法可在下方留言。

pipeline.exe v.2.3.0.0.140640(c) 2008 Pacific Biosciences
 
Primary Analysis Pipeline Execution Engine
 
Arguments:
 
movieFile (Optional, Type:[String])
 
Source movie file to analyzed
 
Options:
 
--sanity
(Type: Flag, Value Type:[Boolean])
SanityTesting
 
--noCCS
(Type: Flag, Value Type:[Boolean])
Do not run circular consensus
 
--on-instrument
(Type: Flag, Value Type:[Boolean])
The pipeline is running on the PAP.
 
--metadata
(Type: Value optional, Value Type:[String])
URI of metadata XML file, contains all needed parameters for an analysis run
 
--t2pConfig
(Type: Value optional, Value Type:[String])
Override the TraceToPulse configuration file
 
-k, --kvp
(Type: 0 to many values accepted, Value Type:[String])
Arbitrary key/value pairs of form 'key=value' that can be used to customize pipeine (internal use only)
 
-c, --config
(Type: Value optional, Value Type:[String])
Config XML file
 
-p, --protocol
(Type: Value required, Value Type:[String])
Protocol to execute
 
--duration
(Type: Value optional, Value Type:[Int32])
Duration (sec) of trace analysis (TraceToPulse)
 
--t2pHotstart
(Type: Value optional, Value Type:[String])
Hot-start TraceToPulse training with weights from this t2p config file
 
--debug
(Type: Flag, Value Type:[Boolean])
Flag for development debugging
 
-n, --numThreads
(Type: Value optional, Value Type:[Int32])
Override the number of threads of the pipeline. Set to -1 to use all processors
 
--help
(Type: Flag, Value Type:[Boolean])
Display usage information
 
--zmwStart
(Type: Value optional, Value Type:[Int32])
First ZMW in a range to process
 
--spikeControl
(Type: Value optional, Value Type:[String])
Name of spike-in control template
 
--zmwBlock
(Type: Value optional, Value Type:[Int32])
Block size of ZMW hole numbers in a range to process
 
--version
(Type: Flag, Value Type:[Boolean])
Version
 
--zmwCount
(Type: Value optional, Value Type:[Int32])
Number of ZMW blocks in a range to process
 
--zmwStride
(Type: Value optional, Value Type:[Int32])
Stride on ZMW hole number in a range to process
 
--startReports
(Type: Value optional, Value Type:[String])
Reports Folder to get a pulse file from - for protocols that do not run pulse calling
 
--maxFrames
(Type: Value optional, Value Type:[Int32])
Maximum number of frames to process (MovieToTrace, deprecated)
 
-a, --adapter
(Type: Value optional, Value Type:[String])
Override the adapter sequence used in Circular Consensus Sequencing. Should be reverse complement of expected read.
 
--trainingSet
(Type: Value optional, Value Type:[String])
Override the PulseToBase training with files from this training set
 
--startTime
(Type: Value optional, Value Type:[Int32])
Offset (sec) at which to start trace analysis (TraceToPulse)
 
-r, --reports
(Type: Value optional, Value Type:[String])
Override the reports folder that pipeline results will be written to
 
--override
(Type: 0 to many values accepted, Value Type:[String])
PipelineOverrides
 
-b, --baseliner
(Type: Value optional, Value Type:[String])
Override the TraceToPulse baseliner





文件名称:Pacbio RS II Primary Analysis Tools

更新日期:2017-04-18

作者信息:Pacbio

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