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.
This is my first blog post in years - primarily down to a second child who is now a toddler. And what better topic to return to than a mainstay of past content, NCBI BLAST? This time with a motivating example from my recent work, metabarcoding. This is term used for sequencing a diagnostic region of DNA using specific primers for a group of organisms of interest, and then matching that amplicon to a database of known species. Human interpretation of a BLAST search can generally put a good guess as the organism - weighing hits and annotated taxonomy (e.g. ignoring the odd suspicious uncultured "fungal" match).
This post is about how sometimes BLAST on the NCBI website can miss 100% identical (albeit not full length) matches, returning instead lots of very good but longer matches. Basically the online defaults don't suit this use-case.
