Why LASTZ Align Sequences in a So Long Time

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3.8 years ago

yunzhe.jiang97 • 0

Hi, everyone.

I am using LastZ to do sequence alignments ( 20 thousand short candidate sequences against a whole genome). However, it took the program nearly a week to do the alignment and it seems that it is still running. Does anyone know whether something goes wrong?

Many thanks.

LastZ alignment • 900 views

ADD COMMENT • link 3.8 years ago by yunzhe.jiang97 • 0

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Is there a specific reason you are using lastz? It was originally designed to align chromosome sized sequences. Use a normal aligner like bwa, bbmap instead.

ADD REPLY • link 3.8 years ago by GenoMax 148k

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LASZT works faster than BLAST, and that is why I use it

ADD REPLY • link 3.8 years ago by yunzhe.jiang97 • 0

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LASTZ and BLAST are not really equivalents, they have different typical usecases. Genomax is right that LASTZ is generally intended for a smaller number of longer sequences.

Doing multiple pairwise alignments against a genome would be a BLAST task really. If BLAST isn't fast enough for you, you could take a look at DIAMOND.

How big is the genome you're aligning against, and how 'short' are the sequences you're aligning?

ADD REPLY • link 3.8 years ago by Joe 21k

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