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.
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