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-   -   Which PacBio ouputs use to do novo assembly? (http://seqanswers.com/forums/showthread.php?t=89656)

ThiBei 06-06-2019 03:42 AM

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.

GenoMax 06-06-2019 04:08 AM

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.

ThiBei 06-06-2019 04:19 AM

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)


https://scontent-lhr3-1.xx.fbcdn.net...40&oe=5D86659A

wrowell 06-06-2019 09:16 AM

Import your metadata.xml file as "RSII Metadata (XML)" data type.


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