I came across a new paper today:

QuasR: quantification and annotation of short reads in R

When I see such papers, I always want to know 'what do you consider short?'. This particular paper makes no attempt to define what 'short' refers to, with the only mention of the 'S' word in the paper being as follows:

Finally, qAlign stores metadata for all generated BAM files, including information about alignment parameters and checksums for genome and short read sequences

There are hundreds of papers that mention 'short read' in their title and many more which refer to 'long read' sequences.

But 'short' and 'long' are tremendously unhelpful terms to refer to sequences. They mean different things to different people, and they can even mean different things to the same person at different times. I think that most people would agree that Illumina's HiSeq and MiSeq platforms are considered 'short read' technologies. The HiSeq 2500 is currently capable of generating 250 bp reads (in Rapid Run Mode), yet this is an order of magnitude greater than when Illumina/Solexa started out generating ~25 bp reads. So should we refer to these as long-short reads?

The length of reads generated by the first wave of new sequencing technologies (Solexa/Illumina, ABI SOLiD, and Ion Torrent) were initially compared to the 'long' (~800 bp) reads generated by Sanger sequencing methods. But these technologies have evolved steadily. The latest reagent kits for the MiSeq platform offer the possibility of 300 bp reads. However, if you perform paired end sequencing of libraries with insert sizes of ~600 bp, then you may end up generating single consensus reads that approach this length. Thus we are already at the point where a 'short read' sequencing technology can generate some reads that are longer than some of the reads produced by the former gold-standard 'long read' technology.

But the read lengths of any of these technologies pales into comparison when we consider the output of instruments from Pacficic Biosciences and Oxford Nanopore. By their standards, even Sanger sequencing reads could be considered 'short'.

If someone currently has reads that are 500-600 bp in length, it is not clear whether any software tool that proclaims to work with 'short reads' is suitable or not. Just as the 'Short Read Archive' (SRA) became the more-meaningfully-named Sequence Read Archive, so we as a community should banish these unhelpful names. If you develop tools that are optimized to work with 'short' or 'long' read data, please provide explicit guidelines as to what you mean!

To conclude:

There are no 'short' or 'long' reads, there are only sequences that are shorter or longer than other sequences.