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Whole genome fasta file for Macaca fascicularis

I would like to align reads to the genome of the Macaca fascicularis monkey. Until now, the genomes I worked with appeared in the Illumina iGenomes page:

https://emea.support.illumina.com/sequencing/sequencing_software/igenome.html

And so I had the WholeGenomeFasta/genome.fa file to work with (from which I created the STAR index etc). However, there is no iGenome for Macaca fascicularis and so I downloaded the fasta files from the Ensembl site, under "Download DNA Sequences":

https://www.ensembl.org/Macaca_fascicularis/Info/Index

Which are all the files here:

http://ftp.ensembl.org/pub/release-104/fasta/macaca_fascicularis/dna/

I'd like to create a single genome.fa file that is similar to the one from iGenomes. My question is: should this be done simply by concatenating the *dna.primary_assembly fasta files?

Thanks a lot! :)

Daniella

fasta macaca fascicularis
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updated by GenoMax GenoMax • written by dani.tom • dani.tom

1 answer

Use top level genome fasta file that contains the entire genome in a single file (LINK). It is available in the directory you linked above.

Here is relevant note from Ensembl README file:

If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent.

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written by GenoMax GenoMax

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