I am relatively new in denovo assembly research. I started with 2X100 Illumina data and have used Valvet to generated contigs for identification of bacterial genome. I have ref genome. The idea is to check presence of absence of bacteria in different samples.
My question is once I have contigs what should be my next step to conclude that the said bacteria is present or absent. I was thinking if I can just blast these contigs or align with refrefnce?
How would I found out which Contig is significant which is not.
Is there any rule to check which contig has to be used before I should check their % alignments with ref.?
Any other sophisticated method of confirming if bacteria is present of absent from such seq data, any member may have used in this forum.
My question is once I have contigs what should be my next step to conclude that the said bacteria is present or absent. I was thinking if I can just blast these contigs or align with refrefnce?
How would I found out which Contig is significant which is not.
Is there any rule to check which contig has to be used before I should check their % alignments with ref.?
Any other sophisticated method of confirming if bacteria is present of absent from such seq data, any member may have used in this forum.