contigs or reads for sequence search in a metagenomics run

[rathankar]

Dear all
I have a doubt:
In a metagenomics experiment, we have reads sequenced from an environmental sample.

Analysis:
1. assemble these reads and get contigs
2. search these contigs against the nucleotide database to get the bacteria present in the sample
3. arrive at a dendrogram to know the family origin


instead of searching the contigs, can we search only the reads. pls reply
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[westerman]

Yes. Read mapping alone will be fine. Assuming that your reads are long enough (50+ bases) to be unique between species. The advantage with contigs is that you will be doing a smaller search since the number of contigs should be much less than the number of reads.