I used Spades for assembling short reads.
in the Spades_output, i have two files "final_contigs.fasta" and "final_contigs.fastg".
what's the fastg format?
and what file should I take for my research?
If you read carefully the SPAdes manual, you will find a link to the FASTG format specification. Its first paragraph:
This document introduces a prototype format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. It is called FASTG, like FASTA, but the G stands for 'graph'.