Question: Capturing whole gene sequences from WGS metagenomics sample
gravatar for Lina F
2.8 years ago by
Lina F160
Boston, MA
Lina F160 wrote:

Hi all,

I have a metagenomics dataset and I am interested in retrieving full or nearly complete gene sequences.

I first tried assembling the data using Ray Meta to assemble the data. The average length of my contigs is between 700 and 900 bp long.

How can I further resolve these contigs?

My first thought was to use a tool like GATTACA to bin the contigs into groups of sequences that might denote species and then try and run an assembly program just on those groups.

Any feedback or suggestions for different approaches are appreciated!

ADD COMMENTlink modified 2.8 years ago by Sej Modha4.6k • written 2.8 years ago by Lina F160
gravatar for Sej Modha
2.8 years ago by
Sej Modha4.6k
Glasgow, UK
Sej Modha4.6k wrote:

If you have assemblies from two separate assemblers then you can try GARM.

ADD COMMENTlink written 2.8 years ago by Sej Modha4.6k
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