Many of you are familiar with EMIRGE, a software for reconstruction 16S rRNA genes from shotgun data. I've been trying to use EMIRGE for my own research, however the software is buggy and not that well supported. I've seen Megraft but authors claim it's not going to work well with data from Illumina.
Are there any other packages worth trying? I like a lot the idea of targeted reconstruction (saves time and increases sensitivity), but there no software packages to choose from to solve that task.
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Pawel Szczesny
I think I've done something like what you want. Just create a multifasta file of genes that you would like to recover and then map your reads to it using something like Smalt, Bowtie, or BWA. Create a consensus sequence of the output sam files using samtools and vcfutils.pl.
I think that Nesoni could do this all-in-one using the shrimp mapper and samtools.
Thanks. This might work for genes which are relatively uniform in terms of selective pressure. For 16S rRNA I don't see how could I map the reads and accurately recover consensus sequence given the structure of the gene (highly conserved regions mixed with hypervariable). But still, it's a good start.
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