Question: Can you automatically detect if reads are from Illumina or IonTorrent?
1
gravatar for Jeroen Van Goey
4.3 years ago by
Jeroen Van Goey2.2k
Ghent, Belgium
Jeroen Van Goey2.2k wrote:

When using the SPAdes Genome Assembler, you can use either the BayesHammer read error correction tool for  Illumina reads or the IonHammer read error correction tool for IonTorrent data.

I want to use SPAdes in a general workflow and I want to know if there is an automatic way to determine if reads are either from Illumina or IonTorrent (without asking the user) so that I can select the correct read error correction tool.

 

 

 

spades assembly • 1.7k views
ADD COMMENTlink modified 4.3 years ago by arno.guille400 • written 4.3 years ago by Jeroen Van Goey2.2k

Can you assume that no one has messed with the input read names in any way?

ADD REPLYlink written 4.3 years ago by Devon Ryan88k

Input names could be changed, so I would prefer a technique that looks at the data itself. However, if that is not possible, looking at the input names might be my only/best bet.

 

ADD REPLYlink written 4.3 years ago by Jeroen Van Goey2.2k

about that - yeah- one shouldn't actually change read names - there is valuable information there

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Istvan Albert ♦♦ 79k
6
gravatar for arno.guille
4.3 years ago by
arno.guille400
France
arno.guille400 wrote:

To determine if the reads are from illumina or IonTorrent, i think the best solution is to look at the read names format in the fastq files.

Illumina reads :

@M02681:36:000000000-AAUMD:1:1101:17649:1746 1:N:0:1

@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index sequence>

 

Ion Torrent reads :

@I7HE0:00523:00720

 

 

ADD COMMENTlink written 4.3 years ago by arno.guille400
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