Which PacBio ouputs use to do novo assembly?

ThiBei · 06-06-2019, 04:42 AM

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 · 06-06-2019, 05:08 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, 05:19 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)

wrowell · 06-06-2019, 10:16 AM

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

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06-06-2019, 04:42 AM	#1
ThiBei Junior Member Location: France Join Date: Jun 2019 Posts: 3	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.

06-06-2019, 05:08 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	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.

06-06-2019, 05:19 AM	#3
ThiBei Junior Member Location: France Join Date: Jun 2019 Posts: 3	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)

06-06-2019, 10:16 AM	#4
wrowell Junior Member Location: Bay Area, CA Join Date: Mar 2017 Posts: 1	Import your metadata.xml file as "RSII Metadata (XML)" data type.