Hi All, I have a very large set 100mer nucleotide sequences (over 20 million) that I'd like to align versus a large number of reference bacterial genomes. I am looking for exact matches as well more distant matches up to 10 mismatches. Should I use megablast or blat?
Are there any documents or literature that someone could point me to that contains comparisons.
I need to stick with either megablast or blat for the moment.
There is so much stuff out there about alignments but I cannot find comparisons. Thanks!
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a615ebfb •
2 answers
I guess it should be possible to select only the desired mappings by parsing the CIGAR strings.
Alternatively, https://github.com/smarco/gem3-mapper allows you to filter mappings by precise global alignment identity, which in this case should be 90-100%
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Consider the following for
blat:You may want to use
magicblastwith 100 mer nucleotides instead: https://ncbi.github.io/magicblast/