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hsinnan75 / GSAlign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
MIT License
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Sequence alignments appear incomplete #19

Open paulamool opened 2 years ago

paulamool commented 2 years ago

Hi hsinnan75

I am currently using GSAlign for genome (~40 Mb each) alignments. I did a quick check on two sequences (available from NCBI) and it seems that the alignment is not complete? Please see attached dot plots. Any help or suggestion would be greatly appreciated.

Best regards, Paula

Using: v1.0.22 GSAlign downloaded on 31/05/2022 Commands: 

GSAlign -r  CM025799.1.fa -q CM025819.1.fa  -no_vcf -t 16 -idy 70 -sen -alen 50 -ind 20 -fmt 1 -dp -o gsa
nucmer -p nuc CM025799.1.fa CM025819.1.fa
mummerplot  --color --fat --layout -t "png" -p nuc nuc.delta

GSAlign.pdf