adding a contig fasta to reference genome fasta

Question

[Elisa]

Hi everyone,

I'd like to add 'chr1_KI270763v1_alt.fa' (929.9 kB) sequence to my reference genome 'genome.fa' (grch38-3.2 GB). Is it possible and which tool shall I use ?

Thank you

Answer 1

[GenoMax]

Simply cat the two files together like so cat genome.fa alt.fa > new.fa (assuming they are both in fasta format).

[d-cameron]

Remember that you'll need to regenerate new index files for this this new reference (.fai, .bwt, etc).