How to use MSU7 rice genome as reference as there has fasta file format.

Question

[Mainul]

I am working with Whole-genome sequence analysis. I have to use the MSU7 rice genome as a reference. Once I going to download reference seq from this site (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/). I am not getting any fasta file format. there got gff and another file format that I am not familiar with. Anyone please help where I get MSU7 reference seq with the fast format. I am using the GTAK pipeline for the assembly. Thanks in advance.

Answer 1

[ATpoint]

The README says:

all.con: complete genome sequence for each of the 12 pseudomolecules, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

Try that and be sure to read documentation.

[Mainul]

all.con is a complete genome sequence but is it a sequence to use alignment on BWA. as BWA only supports .fa file.

[ATpoint]

It is fasta format. It is ready for use with bwa or any other aligner. It is indeed not common to name a file .con but there is no strict rule about this. This below is fasta format regardless of the suffix:

> name
sequence

[Mainul]

Thanks, for your information.