Hi,
I have managed to get a reasonable assembly of a bacterial genome using newbler based on 454 NG sequence data.
I have also available paired end reads for the same bacterial genome and I am wondering is there a way to improve the contigs and scaffolding.
I read about AMOS-hybrid, http://www.biomedcentral.com/1471-2164/11/242, but it requires mates file, which I do not have available instead I have one sequence file for each of the paired ends.
I also thought to try mira but it also requires mates files. Should I request the vender for mates file or there are other software available that can use contigs from my newbler run and raw paired end files and their qualities?
I hope other people may have gone through hybrid assembly issue already and may be of help.
Regards,
Intikhab
I have managed to get a reasonable assembly of a bacterial genome using newbler based on 454 NG sequence data.
I have also available paired end reads for the same bacterial genome and I am wondering is there a way to improve the contigs and scaffolding.
I read about AMOS-hybrid, http://www.biomedcentral.com/1471-2164/11/242, but it requires mates file, which I do not have available instead I have one sequence file for each of the paired ends.
I also thought to try mira but it also requires mates files. Should I request the vender for mates file or there are other software available that can use contigs from my newbler run and raw paired end files and their qualities?
I hope other people may have gone through hybrid assembly issue already and may be of help.
Regards,
Intikhab
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