I have two full genome sequences (in Fasta format) plus annotation file (in gff format) from same organism. One sequence is the reference genome and another is my test sequence.
Would you please suggest me some pipeline or tools ( preferably, R or bash based tool) by which I will be able to generate following results by comparing test seq against reference seq:
- List of mutations in nucleotide and protein level along with their positions.
- List of SNPs and their positions
- List of indels and their positions
I will apply same pipeline for many other test sequences in Fasta format.
NB: I don't have short reads (in Fastq format with quality) for these sequences. So I have to perform the anaysis by plain Fasta files.
Thanks in advance.