Alignment of genomic data

Question

[mittu1602]

Hello, I have fungi genome sequenced data in FASTA format which is 20mb in size and I want to align my data with Diaporthe ampelina which is 40mb in size. I am looking for a tool apart from BLAST. I have already tried YASS tool but it does not work with such large data, it does work finely with small data, I am looking for similar type of tool which can work with my large data.

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Thank you, Meetali

Answer 1

[Felix Francis]

MUMmer: http://mummer.sourceforge.net/manual/

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

mugsy: http://mugsy.sourceforge.net/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031037/

[mittu1602]

Thank you Felix,

MUMmer worked too well for my work.

[WouterDeCoster]

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Answer 2

[Pierre Lindenbaum]

try LASTZ ? https://www.bx.psu.edu/~rsharris/lastz/

[mittu1602]

Hello, Pierre LASTZ worked too but the result files were not well interpreted, Thank you.