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

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
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updated by Ram Ram • written by Jeroen Van Goey Jeroen Van Goey

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

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written by Devon Ryan Devon Ryan

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.

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updated by Ram Ram • written by Jeroen Van Goey Jeroen Van Goey

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

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written by Istvan Albert Istvan Albert

1 answer

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
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updated by Ram Ram • written by arno.guille arno.guille

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