i have whole genome of camel that sequenced via illumina hiseq, i want to assemble this genome in chromosome level. there is no chromosome level assembled genome for camelid, is there any way to do this project?
i have many question in bioinformatics and i am here to learn, thank you in advance
As @Ram already mentioned, what you are looking for is "de novo assembly". See previous discussion here where you can hopefully learn a lot:
I should point out that you are not going to get full chromosomes based on Illumina short reads alone. It's usually not possible to get contigs longer than a few megabases (mammalian chromosomes are hundreds of megabases).
In general, de novo assembly is extremely difficult. There are already existing assembled camel genomes that you can use:
Why not align to those?
There are three camel genomes available (arabian, bactrian and wild bactrian) at NCBI. So at a minimum you should be able to align your data to those. As indicated by @igor even if you are not able to assemble your data at chromosome level, you should be able to get a reasonably good picture of what the genome you sequenced looks like by doing this analysis.
I assume by annotation, you need to assign alignments to a particular gene. If that's the case, you don't need complete chromosomes. Often people use both DNA and RNA for published assembly. Even highly fragmented genome assembly is likely to have reasonable gene annotation.
Even if you sequence chromosomes separately, you are not likely to get a fully assembled chromosome using short reads.
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What you are trying to do is called "de novo genome assembly". I'd recommend you look around a bit on that topic - it's quite interesting. Check out de bruijn graphs and Dan Zerbino's work - that should give you a starting point.