References saying that BWA is not quite specific

Question

[marongiu.luigi]

Hello,

is there a reference stating that BWA MEM is fast and popular but is less specific than BLAST?

Thank you

[GenoMax]

What do you mean when you say less specific than BLAST? Both are aligners but they are meant to be used for specific applications. NGS data aligners generally do global alignments where as Blast does local alignments.

From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425171/ :

Although older alignment software such as BLAST [7] or BLAT [50] can be used to map short reads to a reference genome, those methods are simply too slow. The sheer amount of data, sometimes comprising billions of short reads that have to be aligned to a large (e.g. mammalian) genome, has required innovative new algorithms that run orders of magnitude faster, at least for the specialized problem of short-read alignment to a fixed reference genome.

Answer 1

[Istvan Albert]

The tools implement different algorithms and are designed for completely different use cases:

• BLAST is a local aligner designed to find all high scoring matches.

• bwa mem is a semi-global aligner designed to find the single best match.

Applying the correct tool for the correct task is not related to popularity.

By the way, there is no way bwa is more popular than blast in general.

Not that popularity matters, just to set the record straight, far many more people use (need) blast over bwa.

[marongiu.luigi]

Fair enough. I am asking because I am aligning against viral genomes. I first used BWA MEM and obtained mapping against 1800 viral species. To avoid the possibility of false positives, I then re-rum the mapped reads with Blastn and Blastx in sequence and obtained 46 species. How can I explain the loss of about 90% of the retrieved species? Tx