fasta file parsing

Question

[manaswiniparija3]

I have a genome file in .Fasta format and a file containing some sequences' starting and end positions. how to extract these sequences from the genome file?

Answer 1

[nhaus]

Take a look at bedtools getfasta function. This should do exactly what you want.

[manaswiniparija3]

Thank you

Answer 2

[GenoMax]

You can also use samtools faidx or seqkit faidx.