Dear all,
I recently started working on soil metagenomics data and I am pretty ignorant in this area. I am trying to assign some NGS reads (Solid, Illumina, 454) to some reference bacterial genes I am interested in. For each of the reference gene, I have got hundreds of sequences that I have already aligned and now I would like to check if some of my reads corresponds these alignments.
As far as I know the taxonomic diversity of my samples are very high so I don't expect a very good coverage. So my first question is, is there a point to assemble my reads first ?
And my second question is, which tool would you recommend to assemble reads against multiple sequences ?
Regards,
Michael
I recently started working on soil metagenomics data and I am pretty ignorant in this area. I am trying to assign some NGS reads (Solid, Illumina, 454) to some reference bacterial genes I am interested in. For each of the reference gene, I have got hundreds of sequences that I have already aligned and now I would like to check if some of my reads corresponds these alignments.
As far as I know the taxonomic diversity of my samples are very high so I don't expect a very good coverage. So my first question is, is there a point to assemble my reads first ?
And my second question is, which tool would you recommend to assemble reads against multiple sequences ?
Regards,
Michael
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