Question: How to recover a 16S rRNA gene from genome reads?
0
gravatar for fhsantanna
13 months ago by
fhsantanna390
Brazil
fhsantanna390 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 • 995 views
ADD COMMENTlink modified 3 months ago by felipe.zoujiro20 • written 13 months ago by fhsantanna390
4
gravatar for Chris Fields
13 months ago by
Chris Fields1.9k
University of Illinois Urbana-Champaign
Chris Fields1.9k 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 13 months ago by Chris Fields1.9k
1
gravatar for cschu181
13 months ago by
cschu1811.1k
cschu1811.1k 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 13 months ago by cschu1811.1k

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

ADD REPLYlink written 13 months ago by fhsantanna390
0
gravatar for felipe.zoujiro
3 months ago by
felipe.zoujiro20 wrote:

Hi, you can/could use Metaxa2 (http://microbiology.se/software/metaxa2/). It is a software for extracting 16S rDNA reads from metagenomic/genomic reads. I have used it and worked pretty good.

ADD COMMENTlink written 3 months ago by felipe.zoujiro20
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