Reconstruction of gene using specific reads from shotgun metagenome

Question

[Y.A.T.]

Hi. I'm wanting to reconstruct gene from shotgun metagenome reads, but using only a specific read. Anyone know a good analysis tool for it?

Best Y.A.T.

Answer 1

[colindaven]

I don't think a tool exists for this. People would normally reconstruct the metagenome, providing contigs from various microorganisms in the sample. Then they annotate these contigs and/or search for specific genes in them.

[Y.A.T.]

I see. Then is there any way to search for contigs using specific reads after the binning process? Sorry I'm new to metagenomes.

[colindaven]

Just use a text editor/ grep / blast after assembly. But I suggest you just read up on some literature first, eg current papers and what they use, a metagenomics review etc