Merge Velvet Assemblies

Question

[Rahul Sharma]

Dear experts, I have 3-4 nice velvet assemblies from different k-mer's. I want to merge all these assemblies into a single one. I was trying to do this using Minimus2 or Minimus2-Blat. Can anybody please suggest me any other nice tool/method to do this? And would it be nice to do Scaffolding of velvet scaffolds(As I turned on the scaffolding option during the velvet run) with Minimus2(can also work on N's) ? I would really appreciate your comments. Best regards, Rahul

Answer 1

[Damian Kao]

You can try:

GAM - [?]http://services.appliedgenomics.org/software/gam/index.html[?]

Zorro - [?]http://www.lge.ibi.unicamp.br/zorro[?]

[Rahul Sharma]

Thanks DK for your valuable comments

Answer 2

[Darked89]

Not tested:

• MAIA http://bioinformatics.oxfordjournals.org/content/26/18/i433.short (Matlab...)

• Oslay
  http://ab.inf.uni-tuebingen.de/software/oslay/

• Trans-Abyss
  http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

[Rahul Sharma]

Thank you so much for your valuable comment,, I will try these tools :)