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Old 06-06-2019, 03:42 AM   #1
ThiBei
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Location: France

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Default Which PacBio ouputs use to do novo assembly?

Hello, I was given all the outputs of the result of a whole genome sequencing of a bacteria, and there is a lot of them and I donít understand which one of these I should use to do a novo assembly:
  • 3 *.subreads.fastq
  • 3 *.subreads.fasta
  • 3 *.bax.h5
  • 1 *.bas.h5
  • 1 *.mcd.h5
  • 1 *.metadata.xml


I was thinking using SMRT link to do the analysis , but I donít know which one of these I should use.

Thanks in advance.
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Old 06-06-2019, 04:08 AM   #2
GenoMax
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If you are planning to use SMRTlink then use the bax and bas files.

There are other options like flye (https://github.com/fenderglass/Flye ) and canu (https://github.com/marbl/canu) that may be better than SMRTlink and they can use the fastq files.
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Old 06-06-2019, 04:19 AM   #3
ThiBei
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Thank you for your answer

I allready try canu but for somme resons it dosn't get installed...
I will try to have a look at flye

But for SMRT link I don't understand to what the bas and bax files correspond to (see image)


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Old 06-06-2019, 09:16 AM   #4
wrowell
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Import your metadata.xml file as "RSII Metadata (XML)" data type.
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