Dear list 1) I have illumina short reads from which I want to call SNPs WITHOUT using a reference genome. That is, I want to align the reads among themselves, and then screen each alignment for polymorph positions (SNPs) by taking into account base call quality. Is there a program that would allow building such alignments without reference genome, and that produces output that can be input to R/bioconductor? 2) Generally, are there R/Bioc implementations for SNP-detection using base-call quality? Daniel Berner

dear Daniel, I would suggest to create a consensus of your seqs in order to create a "dummy genome", I don't know the design of your experiment. Did you sequence the whole-genome? what is your sequencing depth? if you have sequencing depth >30x I would use velvet, but check other software for assembly, maybe there are others more recent and which not require that much sequencing depth. That I know, there are no Bioconductor tools for this, but you have tools to do sequence filtering in Bioconductor and after than you make the assmbly. Then after creating your dummy genome I would align the reads to this dummy genome using MAQ. MAQ maps the reads to your ref genome and then you can also use it to identify SNPs. The creators of MAQ have developed another aligner called BWA, which I haven't used but comparing studies have shown that is very good and is faster then MAQ I think. These two aligners allow you to map reads to your dummy genome and take into account the quality scores. Other aligners like Bowtie are possible but don't use quality scores. Then in Bioconductor there are packages to take in the output and make some statistcs from it. Regards, Andreia On Tue, Nov 16, 2010 at 8:11 AM, <daniel.berner@unibas.ch> wrote: > Dear list > 1) I have illumina short reads from which I want to call SNPs WITHOUT using > a reference genome. That is, I want to align the reads among themselves, and > then screen each alignment for polymorph positions (SNPs) by taking into > account base call quality. Is there a program that would allow building such > alignments without reference genome, and that produces output that can be > input to R/bioconductor? > 2) Generally, are there R/Bioc implementations for SNP-detection using > base-call quality? > Daniel Berner > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- -------------------------------------------- Andreia J. Amaral Unidade de Imunologia Clínica Instituto de Medicina Molecular Universidade de Lisboa email: andreiaamaral@fm.ul.pt andreia.fonseca@gmail.com [[alternative HTML version deleted]]