Which PacBio ouputs use to do novo assembly?

[ThiBei]

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 don’t 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 don’t know which one of these I should use.

Thanks in advance.

[GenoMax]

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]

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)

[wrowell]

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