What the difference between last-split and single2_cov
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15 months ago

I want to obtained a multiple alignment between some genomes by using TBA. First I used lastal of LAST to make pair-wise alignment of genomes. Then, I used single2_cov of TBA to find the returns only those alignments that are single coverage.

lastal -C2 -E0.05 ~/WORK/TBA/DB/A/A..db ~/DATABASE/D/D.fna \
|tee|cat <(echo "##maf version=1") -|single_cov2 /dev/stdin > A.D.sing.maf


But, I found the single2_cov readed all data into memory, whose size beyond 100+ Gb. My server does not have such a large memory.

And I found the last-split finds a unique best alignment for each part of each read. It seems that the single2_cov and last-split have similar function. And latter uses less memory.

So can I use last-split instead of single2cov ?

Best wishes!

MSA TBA LAST • 298 views