make a reference genome for BRIG (pan-genome analysis)

Question

[pascalandres182]

Hi all I'm doing a pan-genomics study, which as a final step I use the BRIG program to represent the genome globally. The problem is that I need to generate a reference genome that reprecente the 28 different strains that use, to represent important elements such as phages and deletions in the genome. if the question would be how do I make a reference genome that contains all of these elements in some way? Thank you

Answer 1

[goodez]

The reference genome will be in fasta format right? You can simply cat genome1.fa genome2.fa genome3.fa . . . > genomes.fa

One caveat is that each fasta header needs a unique name. For example, there may be chr1 in multiple genomes. So you may need to make them unique, such as: chr1_genome1 and chr1_genome2.

Let me know if I'm misunderstanding your question.