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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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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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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 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.
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