Which reference genome to use?

[michaellim]

For most purposes, you should use the most closely-related genome, even if it is not a single-contig assembly. I'm not sure what you mean by "sequence type" though.

Hi Brian,

For example with E. coli, although this is ONE species, but there are various version of it, i.e. sequence type (ST), for example the human adapted E. coli which causes problematic infections around the world is ST131. Between the different sequence types, there might be mutations/genes specific to each of them.

I'm totally new to sequencing. When they are in several contigs, does it mean that there are gaps between the sequences, hence the authors deposited the sequences in contigs rather than a circular 4Mb chromosome?

Many thanks for the advice.

[AntonioRFranco]

You can do a whole genome comparison with some programs such as Mauve or Act. There are tutorials around explaining how to use them

[Brian Bushnell]

For most purposes, you should use the most closely-related genome, even if it is not a single-contig assembly. I'm not sure what you mean by "sequence type" though.

[michaellim]

Dear everyone,

I am doing RNA sequencing on a bacteria, but I am unsure which type of reference genome to use for my RNAseq data. Currently, there are two options:

1. A complete and annotated reference genome of a bacteria from a different sequence type.

2. A newly published genome of the same sequence type as my bacteria, but the genome is separated in several contigs.

I do not know how different are the different sequence type or how many of the genes are specific to the bacteria of my sequence type and not the complete reference genome (option 1). They are all the same bacterial species though.

Which would be more appropriate? Would appreciate some advice.

Thank you.