Question: How to recover a 16S rRNA gene from genome reads?
0
gravatar for fhsantanna
7 months ago by
fhsantanna340
Brazil
fhsantanna340 wrote:

I have sequenced a bacterial genome with Illumina 2x300 pb kit and after that I have assembled the genome using SPADES (and also A5 pipeline).

The problem is that the draft genome does not present a full 1500 pb rRNA 16S gene. It is expected, since assemblers do not do a great deal with repetitive regions.

However, I need the full-length 16S rRNA gene for my research purposes (taxonomy). Is that a way to recover it from the genome reads (>30 x coverage)?

PS: I have found a promising program named Reago, but it did not worked for me. It seems it does not deal with reads over 101 bp.

assembly denovo rrna genome • 511 views
ADD COMMENTlink modified 7 months ago by cschu181640 • written 7 months ago by fhsantanna340
4
gravatar for Chris Fields
7 months ago by
Chris Fields1.8k
University of Illinois Urbana-Champaign
Chris Fields1.8k wrote:

I have used SortMeRNA in the past to filter rRNA, and it has been used for the flip purpose (e.g. retaining only rRNA reads for taxonomic analysis). You could try this in combination with assembly to see if you can get a more-resolved 16s region.

ADD COMMENTlink written 7 months ago by Chris Fields1.8k
1
gravatar for cschu181
7 months ago by
cschu181640
cschu181640 wrote:

I second the SortMeRNA approach from Chris Fields. Alternatively, you could align your reads against an as closely as possible related 16S rRNA sequence and then do guided assembly (StringTie?) or deNovo (using only the aligning reads) from there.

ADD COMMENTlink written 7 months ago by cschu181640

Nice suggestions. I'll give a try. Soon I post a feedback.

ADD REPLYlink written 7 months ago by fhsantanna340
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