FASTQ uploads to ENA FTP site with rclone

I've recently been working what I considered to be a large scale FASTQ upload to the European Nucleotide Archive (ENA), from where it will be mirrored to the NCBS Short or Sequence Read Archive (SRA). Although the total size was "only" 37GB, this was about 3500 pairs of Illumina MiSeq FASTQ files - more than enough to make me worry about the job being interrupted and needing to resume without repeating uploads.

FASTQ must die! Long live SAM/BAM!

I think it is time to retire the FASTQ file format in favour of storing unaligned reads in SAM/BAM format. I will try to explain, as this may not immediately strike everyone as logical, given SAM/BAM is primarily a sequence alignment/mapping format, while for "raw" reads FASTQ is near ubiquitous in Next Generation Sequencing (NGS), more sensibly known as High Throughput Sequencing (HTS).