what is the best tools for assembly or mapping for wheat genome which is sequenced by illumina.we have to files in fastaq format named as R1,R2.
Any NGS aligner (e.g. BBMap, Bowtie2, BWA etc) will be capable of mapping your data against the wheat genome. You can grab a recent build from Wheat Ensembl Plants page. Assembling the wheat genome from Illumina data may be a taller order. Especially dependent on the amount, kind and quality of data you have.
Assembling and mapping are two very different steps. Assembling wheat genome with Illumina might be very hard to impossible. On the other hand, I don't know if the wheat genome is out. I suggest you visit this website to see if the genome is out (I just noticed the reference from genomax, so you might be able to retrieve the genome!). Also, I suggest you start with some good tutorial on NGS data analysis. I found this one that could be useful, but you might give a look, to see if there is something better suited to your needs.
i have two variety of wheat one from Pakistan 2nd from Germany .these two variety sequenced by ilumina and i have reads files.i have to done work to find following 1. Comparative SNPs in different samples 2. Allelic variations 3. Alternative splice variants 4. GOs analysis 5. Functions for stress related genes, root genes, drought genes etc. 6. Pathway analysis especially with respect to root architecture If we find some candidate genes then we can do real-time PCR and other genome editing experiments. i have no knowledge how to do it..kindly tell me step by step how to solve it?
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Can you give a bit more info of what you're trying to achieve? The wheat genome is huge (13GB for the tetraploid, 17GB for the hexaploid variant) and about 98% repetitive. Successful assembly based only on Illumina data (without long mate pairs) is almost impossible.
i have two variety of wheat one from Pakistan 2nd from Germany .these two variety sequenced by ilumina and i have reads files.i have to done work to find following 1. Comparative SNPs in different samples 2. Allelic variations 3. Alternative splice variants 4. GOs analysis 5. Functions for stress related genes, root genes, drought genes etc. 6. Pathway analysis especially with respect to root architecture If we find some candidate genes then we can do real-time PCR and other genome editing experiments. i have no knowledge how to do it..kindly tell me step by step how to solve it?
A forum is not the best place to provide directions to do all of those things you noted above. Instead you should familiarize yourself with basic quality control, scanning/trimming of sequence data, alignments followed by variant calling. Use this paper as a general reference for the basics of how to do this. It may be best to find some local bioinformatics assistance, if you have not done any of this before and/or are not familiar with unix command line.
I don't think you have to assemble anything, at least not as a first step.
Map your reads to an existing genome assembly (s. genomax's answer), then if necessary, assemble the unmapped reads analogously to what they do here: http://www.pnas.org/content/114/6/E913.abstract.
There are two recent 6n wheat (Chinese Spring 42) genomes available: Ours is described in http://genome.cshlp.org/content/27/5/885.full (this should also be the one that genomax is referring to), the other in http://www.biorxiv.org/content/early/2017/07/03/159111 (not sure about the availability of this one, but it reads promising and should be out soon). The next IWGSC build is not yet out.