How do I reduce the length of a contig?
I have recently assembled my shotgun metagenomic reads using metaSPADES without changing any default settings. I then upload them to MG-RAST for annotation. However, some of the samples have contigs greater than the maximum length cut off (500,000bp). According to the manual, the MG-RAST pipeline has a hard time annotating reads/contigs that contain multiple organisms. If I reduce my K-mer size, would this result in shorter contigs? Or does anyone have any other suggestions for adjusting contig length without manually separating them and compromising coverage statistics?
Thank you!
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The best approach is to use a different program that does not have such a strange and arbitrary limitation. But if you need to observe a 500kbp limit, manually separate them, rather than trying to find parameters that make SPAdes give you a bad assembly. You can use BBMap like this:
That will break sequences longer than 500kbp into 500kbp pieces.
Thank you so much! I will try that!
I could not find this mention to the contig maximum length here, could you point the link to the manual and page / section mentioning it?
It is on page 77 in the Data submission via the web interface section.
I could not find any mention to a limit on contig size. Are we talking about the same manual?
MG-RAST Manual for version 4, revision 1. October 3nd, 2016
ftp://ftp.metagenomics.anl.gov/data/manual/mg-rast-manual.pdf
My mistake, that is the page referring to the format. I found out about the bp cutoff after uploading the file. It will not allow you to submit files that contain one or more sequences/contigs who are >500kbp. It will not allow you to select these files for submission on the submit page.
Below is the link to the screenshot of the submission page:
https://ibb.co/jiWHc5