Question: How to recover a 16S rRNA gene from genome reads?
0
gravatar for fhsantanna
3.6 years ago by
fhsantanna490
Brazil
fhsantanna490 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 • 4.3k views
ADD COMMENTlink modified 2.0 years ago by jeremieaauger10 • written 3.6 years ago by fhsantanna490
4
gravatar for Chris Fields
3.6 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k 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 3.6 years ago by Chris Fields2.1k
1

I should add, I've also started looking into phyloFlash for this, which can use SortMeRNA 'under the hood'. Seems very nice.

ADD REPLYlink written 23 months ago by Chris Fields2.1k
1
gravatar for cschu181
3.6 years ago by
cschu1812.5k
cschu1812.5k 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 3.6 years ago by cschu1812.5k

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

ADD REPLYlink written 3.6 years ago by fhsantanna490
1
gravatar for felipe.zoujiro
2.7 years ago by
felipe.zoujiro30 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 2.7 years ago by felipe.zoujiro30
1
gravatar for jeremieaauger
2.0 years ago by
Canada, Montréal
jeremieaauger10 wrote:

I think that you should to use MetaPhlAn!

"MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data."

You are wasting sequencing information by concentrating on 16S only. The software uses all the marker genes available in your data. This software comes from the reputable microbiome software suite "Biobakery".

Check it out! http://huttenhower.sph.harvard.edu/metaphlan

Cheers, Jérémie

ADD COMMENTlink written 2.0 years ago by jeremieaauger10
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