Hi members, I am working on Gut Microbiota. I have isolated my bacteria and have it sequenced by Illumina HiSEQ. They gave me a file that contained reads. Then i contructed contigs outta of that using VELVET. I have 159 contigs of 2.5 MB.Now i want to construct phylogenetic tree from whole genome and do comparative analysis also i have to find plamids if in my seq. For these tasks do i need a whole assembled genome? If yes then how i could get my whole genome. How i would find plasmids from these contigs using a reference genome? And how i would contruct tree that shows its closely related species using contigs-which i dont know are ordered or not? Please give me a optimal solutions of theses queries. I have very short time left for this work.
Question: Genome assembly from contigs assembled by WGS
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sidrairshad29 • 0 wrote:
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Did you do any quality trimming or process the data before using velevt?
Thank you for showing your concern. Here are the details of assembly; Assembly Method :: Velvet v. 28.11.2015 Genome Representation :: Full Expected Final Version :: No Genome Coverage :: 10.0x Sequencing Technology :: Illumina HiSeq ##Genome-Assembly-Data-END#
Also i have done annotation using RAST.
can you please first read
http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html
http://www.sciencedirect.com/science/article/pii/S0167701211002508
this will give a wider idea then we can answer more questions