文件列表:

canu-1.8\addCopyrights-BuildData.pl (3394, 2018-10-23)
canu-1.8\addCopyrights.dat (970524, 2018-10-23)
canu-1.8\addCopyrights.pl (12772, 2018-10-23)
canu-1.8\buildRelease.sh (1736, 2018-10-23)
canu-1.8\documentation\Makefile (6778, 2018-10-23)
canu-1.8\documentation\reST-markup-hints (412, 2018-10-23)
canu-1.8\documentation\source\canu-overlaps.svg (130280, 2018-10-23)
canu-1.8\documentation\source\canu-pipeline-17.svg (196276, 2018-10-23)
canu-1.8\documentation\source\canu-pipeline-20.svg (179580, 2018-10-23)
canu-1.8\documentation\source\canu-pipeline.svg (196094, 2018-10-23)
canu-1.8\documentation\source\command-reference.rst (5570, 2018-10-23)
canu-1.8\documentation\source\commands\bogart.rst (2448, 2018-10-23)
canu-1.8\documentation\source\commands\bogus.rst (183, 2018-10-23)
canu-1.8\documentation\source\commands\canu.rst (1851, 2018-10-23)
canu-1.8\documentation\source\commands\correctOverlaps.rst (1061, 2018-10-23)
canu-1.8\documentation\source\commands\createFalconSenseInputs.rst (37, 2018-10-23)
canu-1.8\documentation\source\commands\erateEstimate.rst (45, 2018-10-23)
canu-1.8\documentation\source\commands\estimate-mer-threshold.rst (118, 2018-10-23)
canu-1.8\documentation\source\commands\fastqAnalyze.rst (722, 2018-10-23)
canu-1.8\documentation\source\commands\fastqSample.rst (1609, 2018-10-23)
canu-1.8\documentation\source\commands\fastqSimulate-sort.rst (212, 2018-10-23)
canu-1.8\documentation\source\commands\fastqSimulate.rst (3060, 2018-10-23)
canu-1.8\documentation\source\commands\filterCorrectionOverlaps.rst (1140, 2018-10-23)
canu-1.8\documentation\source\commands\findErrors.rst (24, 2018-10-23)
canu-1.8\documentation\source\commands\gatekeeperCreate.rst (256, 2018-10-23)
canu-1.8\documentation\source\commands\gatekeeperDumpFASTQ.rst (1157, 2018-10-23)
canu-1.8\documentation\source\commands\gatekeeperDumpMetaData.rst (650, 2018-10-23)
canu-1.8\documentation\source\commands\gatekeeperPartition.rst (334, 2018-10-23)
canu-1.8\documentation\source\commands\generateCorrectionLayouts.rst (833, 2018-10-23)
canu-1.8\documentation\source\commands\leaff.rst (2306, 2018-10-23)
canu-1.8\documentation\source\commands\meryl.rst (6155, 2018-10-23)
canu-1.8\documentation\source\commands\mhapConvert.rst (398, 2018-10-23)
canu-1.8\documentation\source\commands\overlapConvert.rst (360, 2018-10-23)
canu-1.8\documentation\source\commands\overlapImport.rst (710, 2018-10-23)
canu-1.8\documentation\source\commands\overlapInCore.rst (2372, 2018-10-23)
canu-1.8\documentation\source\commands\overlapInCorePartition.rst (93, 2018-10-23)
canu-1.8\documentation\source\commands\overlapPair.rst (825, 2018-10-23)
canu-1.8\documentation\source\commands\ovStoreBucketizer.rst (1285, 2018-10-23)
canu-1.8\documentation\source\commands\ovStoreBuild.rst (1078, 2018-10-23)
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pbutgcns ======== DAG-based consensus caller for celera assemblers unitigs. It is currently tested only using pacbio corrected reads, though in prinicipal it could be used for pacbio un-corrected. It currently uses a simple python adapter to interface with the tigStore. Eventually, this is expected to be replaced with a more direct call to lower-level API calls. Building -------- > make BLASR= > ./pbutgcns -h ### Support libraries needed * [pblibblasr](https://github.com/PacificBiosciences/pblibblasr) BLASR library * [boost](http://www.boost.org/) Popular C++ utility library (1.46 or 1.47) * [log4cpp](http://log4cpp.sourceforge.net/) Logging library (1.0 or 1.1) Running ------- The input is an assembly generated by celera-assembler, typically only through the unitigger stage. However, if you want to compare it to the existing consensus caller, it can be run to completion. Either one will work. A utitilty shell script *pbutgcns_wf.sh* can be used to execute the consensus workflow for a given file containing a list of unitigs ids. Make sure that you have CA's tigStore and gatekeeper utilities, tigStore-adapter.py and pbutgcns in your path. # tmp: temporary directory to generate consensus into # cap: CA-prefix used in celera assembler # nproc: number of threads to use while building consensus # cns: the output file name > tmp=/tmp cap=asm utg=utg.lst nproc=4 cns=utg_consensus.fa pbutgcns_wf.sh

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