methods/tools to compare/alignment two chromosome-level long DNA sequences

Question

[boymin2020]

Hi,

Recently I have been working hard to compare two chromosomes (~21,484,951bp). One is from reference genomics while the other is assembled in our lab. We had tried to use BLAST but failed as they are too long. I am not familiar with this kind of analysis. Would you like to recommend any methods/tools for this job?

Thanks,

[boymin2020]

Thank you a lot, Pierre. I do have the alignment results. Could you also recommend tools to visualize the MAF files? As I have been analyzing the genomics of Bombyx Mori, it seems that IGV of NCBI can not be employed here.

Answer 1

[Pierre Lindenbaum]

LAST : http://last.cbrc.jp/