<p>Is there a better way of downloading the human genome reference sequence in fasta format than downloading it from the UCSC site? <a href='http://bio-bwa.sourceforge.net/'>BWA</a> protocol asks for an index to be created from the human genome reference multi fasta so I want to get this.
Thanks</p>

<p>[Edited for clarification in response to answers and comments:]</p>

[The version][1] used by the 1000 genomes project is recommended. The mitochondrial genome in the g1k version is the most widely used [rCRS][2]. The chromosomes and contigs are concatenated, so it is less likely to make mistakes (people frequently concatenate all sequences including different haplotypes from the same region).

We have seen a lot of complications caused by different chromosome names (chr1 vs. 1) or different ordering (chr2 before chr10 or after). It is true that which b37 version to use does not matter too much, but converging to something close to a standard would reduce a lot of unnecessary works for everyone.

 [1]: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/
 [2]: http://en.wikipedia.org/wiki/Cambridge_Reference_Sequence