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Old 01-27-2015, 02:42 AM   #1
macb
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Default RS_CeleraAssembler not included in SMRT portal v2.3

Hello Guys,
I have recently installed the last version of SMRT Potal (v2.3). I need to run Celera for the error correction on Pacbio reads, however the RS_CeleraAssembler.1 is not included.
Is there a mean to add customized protocol such as RS_CeleraAssemblerl into SMRT Portal ?
Thank you.
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Old 01-28-2015, 06:29 AM   #2
flxlex
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When you choose HGAP, it uses Celera for the error-correction (and assembly).
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Old 01-28-2015, 08:37 AM   #3
macb
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the CeletaAssembler version used by SMRT is 8.1 , I need the 8.2 version which is recommended.
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Old 01-28-2015, 09:33 AM   #4
GenoMax
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Then you will need to use it outside SMRTportal.

Rob Hall (from PacBio) had previously advised to a different poster that it was not simple to upgrade the version included in portal.
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Old 01-28-2015, 10:41 AM   #5
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If you want to run hybrid error correction then I would install 8.2 outside SMRT Analysis. For PacBio only assembly, the protocol in SMRT Analysis (HGAP.3) uses a modified version of 8.1, which will perform the same as 8.2.
The Hybrid assembly protocol was dropped from SMRT Analysis as it's easier and gives better results using the current version of PBcR in CA (8.2)
http://wgs-assembler.sourceforge.net...index.php/PBcR
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Old 02-02-2015, 08:37 AM   #6
macb
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Ok ! Thank you Rob Hall and Genomax
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