Why LASTZ Align Sequences in a So Long Time
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.
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yunzhe.jiang97 •
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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 likebwa,bbmapinstead.LASZT works faster than BLAST, and that is why I use it
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?