Making Scaffolds From Contigs Without Paired Read Information

Question

[Prakki Rama]

Hi all,

Could some one help me knowing how the scaffolding of contigs is done when paired read information is not available?

Thanks in advance.

[Prakki Rama]

For the transcriptome assembly, one can also consider protein sequences of nearest species and can perform scaffolding

Answer 1

[Casey Bergman]

In the absence of any other extrinsic data, paired-read information is required to assemble scaffolds de novo from contigs. However if you have (i) a closely related genome that has been scaffolded or a (ii) physical map you can order and orient contigs into scaffolds by (i) mapping contigs in your assembly to the related genome or (ii) matching sequence tags from your physical map to contigs in your assembly.

[Prakki Rama]

@casey Bergman: Thank you for the answer.

[mariaveronicafumero]

any software to do this? (scaffolding from paired-end reads and contigs, no mate-pairs) thanks!