Why you don't use blast algorithm for read alignment?
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+ blast is just too slow, NGS mappers sacrify quality for speed. Try to align 1E6 50bp reads on a human genome...
+ blast doesn't handle paired-end sequencing, quality, ...
+ blast doesn't (officially) support the standard BAM format -
That's true (as are your other points), but a little misleading. Bear in mind that there are a lot of flavors of BLAST; some of them are designed to convert nucleotides to amino acids and map in protein space, which is not useful for noncoding reads. Also, I would argue that short-read aligners can give higher-quality output than BLAST, despite being optimized for speed. Consider RNA-seq data mapped to a genome, for example - appropriate NGS aligners would give much higher quality output compared to BLAST.Originally posted by lindenb View PostComment
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