Ion Torrent data quality trimming

Question

[vera.korneeva]

Hello!

I need to make contigs from the Ion Torrent data. This is a microbial genome fragment library. It supposed to be a set of 400 bp read. Due to quality reasons (I used FastQC to check) the reads are kind of good for the first 170-200bp. Our core sequencing facility releases the data as *.FASTQ files and the adaptors are supposed to be trimmed. I am not very experienced with NGS data analysis. The only program I used to clean my date was Trimmomatic but at that time I worked with Illumina reads.
Could you suggest me something like Trimmomatic for my Ion-torrent data, please?

Thanks for your tips.

[GenoMax]

Since Ion data is in fastq format trimmomatic should work with it. What kind of cleaning are you looking to do? As I recall, Ion fastq scores are not totally equivalent to Illumina's. Perhaps you could try to use the data you have as is, with say SPAdes for assembly.

[vera.korneeva]

Thank you for your suggestion. The only cleaning I want to perform at the moment is to cut the low quality ends before assembly.

Answer 1

[5heikki]

Optimal would be to use the ubam file straight from the sequencing machine with Spades assembler. You lose valuable information (that Spades utilizes) when you convert the ubam files to fastq.

[Brian Bushnell]

Are you sure about that? The Spades manual does not mention anything about it. It states that bam is allowed for Ion Torrent reads, but not that is preferred or in any way advantageous over fastq; just that for error-correction fasta should not be used (because the quality scores are lost).

[5heikki]

Yes, they use also flow information (obviously not present in fastq) for read error correction. I don't know why it's not in the manual but the main dev has at least communicated as much to me ~2 years ago. Edit. I read through my mail and came to realize that I did not discuss this specific topic with the dev, however, I'm convinced that I read about it somewhere. Also, if you dig through the source, you'll find many references to flow stuff under /src/projects/ionhammer

[vera.korneeva]

Thank you for your advice. Just to make things clear. Do you mean that I should better take completely row reads in bam format with all the adapters and barcodes in it and assemble it with Spades? Does Spades cut all the adaptors and barcodes itself? Sorry, if this is an obvious thing for you. There is nothing about it in the manual.

[5heikki]

I'm talking about the files that are @ /var/www/output/Home at Torrent Server. They have been quality controlled and demultiplexed. These are the same ubam files that can be downloaded also through Torrent Server's web gui.

[vera.korneeva]

Thank you, now everything is clear.