Question about metagenomic assembly

[sf202303]

Hi everyone, I am working on the metagenomic assembly for Illumina 2x250 reads. I found "We suggest using 350-500 bp fragments with 2x150 reads and 550-700 bp fragments with 2x250 reads." (in the section "Assembling long Illumina paired reads (2x150 and 2x250)"). Does that mean I need to trim my reads first and only keep those with 550-700 bp? If so, any recommended trimming tool? Thank you very much.

[asl]

Hello

The suggestion is about fragments not reads. Fragment length distribution is a feature of your sequencing library and really depends on how it was prepared. You may want to talk to your sequencing center about fragment length distribution (aka insert size distribution).

[sf202303]

Thanks for your reply! So the bioanalyzer fragment size could be higher than 700bp? What fragment range may not be preferred?

[asl]

There is no "bad range". Fragment length distribution effectively influences which repeats might be span by these fragments and what you can do around this. E.g. if your left and right reads overlap, then you could resolve only shorter repeats, etc.

[sf202303]

Thanks so much for your help! One more question, where can I learn more about how to adjust the fragment length and/or what are sequencing/fragment parameters to be considered before metaSPAdes assembly?

[asl]

Well, SPAdes is not tuned to a particular properties of the input data, it tries to be robust and estimate from the input fas much as possible.

[sf202303]

Thanks again for all your replies and help!