Program to align scalffold to scalffold?

Question

[carlosgonzalezcruz327]

Hi everyone. I'm trying to align some scalffolds from one fusarium specie to other scalffolds from another fusarium specie, but i have problems to find any program to do it.

i have tried do it with bowtie2 but it didn't work

can someone suggest a program?

i heard about BWA but really i don't know, i'm so new in this.

thank you in advance

Carlos G.C

Answer 1

[GenoMax]

If you have really large sequences then consider using a program like lastz (LINK).

[carlosgonzalezcruz327]

thank you man, i will read about it.

Answer 2

[patrickdm]

Hello, you could try MUMmer4 nucmer, to align the scaffolds, or the dnadiff utility that wraps nucmer and runs other utilities to compare the two genomes and generate reports with alignment stats, SNPs, breakpoints and unique regions.

https://mummer4.github.io/manual/manual.html

[carlosgonzalezcruz327]

hi, thank you so much. I've done it. I used nucmer and all ran fine. then, i used the -show-coords option and now i dont know how get a interpretation of my results (my currently problem). Well, i'm trying to get a good answer.

Thank you again.

[patrickdm]

I'd try mummer's dnadiff utility then, but not knowing the biological problem you're investigating it could be a misleading suggestion (hope it helps anyway)

dnadiff is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species.