Can you automatically detect if reads are from Illumina or IonTorrent?

Question

[Jeroen Van Goey]

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.

[Devon Ryan]

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

[Jeroen Van Goey]

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.

[Istvan Albert]

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

Answer 1

[arno.guille]

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