Avoid using ascp directly for downloads

Avoid using ascp directly for downloads

NCBI has provided Aspera access for many years. Many users have grown accustomed to direct use of ascp. We initially recommended this approach until the prefetch tool became available. Please see https://github.com/ncbi/sra-tools/wiki/HowTo:-Access-SRA-Data .

There are several reasons why direct use of ascp (or curl, wget, etc) is not recommended. The main reason is that they are likely to only retrieve a portion of the data required. prefetch knows how to download the principal file and any auxiliary data that are needed to complete it for offline operation. Another reason is that prefetch knows where to put the downloads according to toolkit configuration.

As of early 2019, the SRA is starting to make use of additional forms of storage media, which are less useful over Aspera's fasp protocol. Files stored in these media may not be accessible via ascp and have triggered creation of some issues to report the problem.

The problem is addressed by using prefetch which is an actively maintained tool that will use https whenever fasp is not available. This is in addition to all of the other benefits of using prefetch.

The moral of the story is use prefetch.