which file to use for alignment?

[lonesome_forager]

Hello,

I'm planning to align some RADseq reads against a genome to identify SNPs, however its the first time i've had to get the reference genome and i can't identify which .fa file is the complete genome from the NCBI website.

Can anyone help please? in wanting the Bombus terrestris genome but it looks like its split into separate files per chromosome, do i need to merge them all to get a single .fa genome file to align my reads to?

here's the ftp folder
ftp://ftp.ncbi.nih.gov/genomes/Bombus_terrestris/

thank you

[GenoMax]

You will need to concatenate the sequence files into one to make the "genome" reference. As to which files to get that is an interesting question.

You could get the RefSeq files from here: ftp://ftp.ncbi.nih.gov/genomes/Bombu...romosomes/seq/ or the *.fa.gz files from individual chromosome directories.

Take a look at the README file about the differences between the two before you decide: ftp://ftp.ncbi.nih.gov/genomes/Bombus_terrestris/README You may have to try both.