How can I ideal with the next generation sequencing in R or bioconductor environment

[nacoo2000]

some software like this:
Alignment Tools
* Eland: http://illumina.ucr.edu/illumina_docs/
* velvet:http://www.ebi.ac.uk/~zerbino/velvet/
* Maq (Mapping and Assembly with Quality): http://maq.sourceforge.net/maq-man.shtml
* SOAP alignment tool: http://soap.genomics.org.cn/
* SeqMaq: http://biogibbs.stanford.edu/~jiangh/SeqMap/
* Bowtie: http://bowtie-bio.sourceforge.net/
* Novoalign: http://www.novocraft.com
* BWA - Burrows-Wheeler Alignment Tool: http://maq.sourceforge.net/bwa-man.shtml
* BWA-SW (general purpose local alignment tool): http://i.cs.hku.hk/~ckwong3/bwtsw/
* Zoom: http://www.bioinformaticssolutions.com/products/zoom/index.php
* SHRiMP: http://compbio.cs.toronto.edu/shrimp/
* SHORE (1001genomes.org): http://1001genomes.org/downloads/shore.html
* CloudBurst (Highly Sensitive Short Read Mapping with MapReduce):
http://apps.sourceforge.net/mediawiki/cloudburst-bio/index.php?title=CloudBurst

[Ariel Paulson]

Sounds like you want to review Martin Morgan's slides on this very topic:

http://www.bioconductor.org/help/course-materials/2010/CSAMA10/BioconductorIntroduction.pdf

This is pretty much the cutting edge of BioC development for next gen seq analysis.

HTH,
Ariel

[Lingsheng Dong]

I use R package SPP for chip-seq analysis. It can read quite a few aligner's output file. Here is the original package tutorial. http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html
Here is my version of the tutorial:
https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/
Hope this helps.
Lingsheng

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