alignment of whole genome sequence

Question

[sh_shaddad77]

I am searching for SNP by doing the alignment for 4 strain downloaded from NCBI genome database Fasta format. while bowtie program commands Fasta format h, which is not available in NCBI.

where I can find fastq?

for more details, I am working on Candida parapsilosis (Fungus) Reference strain CDC317 other strain GA1, CBS1954, CBS6318

can be converted from Fast to Fastq? if the bowtie is not suitable, could please suggest other programs accept Fasta format

.

[Joe]

Are you trying to align reads to a reference genome, or align full whole genome sequences together?

Answer 1

[Mensur Dlakic]

You may want to try MUMmer. Several other tools are listed here.