Downloading a reference Genome for Bowtie2 How do I download a reference genome that I can use with bowtie2? Specifically HG19. On UCSC there are a lot of file options.
It’s a matter of preference I guess but I recommend the Ensembl builds. Decide whether you want the toplevel or primary assembly, and whether you want soft-masked, repeat-masked or unmasked files. The naming schema is very straightforward; the combinations are described in the README file, and all files reside in one directory.

For example, if you want the unmasked primary assembly, the file to download would be Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz.

As for GoldenPath/UCSC, there’s no need to download and concatenate separate chromosomes (contrary to what the other answer said); you can download the whole (toplevel) reference from the bigZips directory; from the README:


  This directory contains the Feb. 2009 assembly of the human genome (hg19,
  GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)),
  as well as repeat annotations and GenBank sequences.


There are essentially three options here:


chromFa.tar.gz, which contains the whole genome in one chromosome per file;
chromFaMasked.tar.gz, the same with repeats masked by N;
hg19.2bit, which is the whole genome in one file, but needs to be extracted using the utility program twoBitToFa, which needs to be downloaded separately.


In any case, I always download the reference and build my own index for mapping, since this allows me more control; not everybody might need this much control, but then building the index once is fairly fast anyway.