Document best use cases versus alternatives

[peterjc]

Would other people find it useful to have a short section in the README file about alternative tools and pro-and-cons? e.g.

• https://github.com/kblin/ncbi-genome-download fetches from FTP so may be faster (?) but restricted to genomes not all nucleotide records
• NCBI Entrez command line tools - complicated command line API, but can download in parralel from AWS so potentially faster
• https://www.ncbi.nlm.nih.gov/sites/batchentrez web-based so can't be scripted
• ENA download options?

I'm currently using ncbi-acc-download in a simple batch script, but finding this isn't nearly as fast as I had hoped with thousands of sequences:

#!/bin/bash
set -euo pipefail

for ACC in `cat acc_list.seq` ; do
    echo $ACC;
    if [ -f $ACC.fa ]; then
	echo Done;
    else
	ncbi-acc-download -e all -F fasta -v $ACC;
    fi;
done
echo "All Done"

Even if not worth adding to the README, a brief discussion here on this issue would be informative. Thank you!

[kblin]

I'm not really in a position to write this comparison, because I don't use any of those tools (apart from ncbi-genome-download)