Scaffolding contigs generated by minia

Question

[Mostafa]

I have a large number of read libraries, doing denovo assembly by minia. The minia generates some files. Does any body know that how is it possible to use the generated file in order to make scaffolds by a scaffolder? any same experience?

Answer 1

[h.mon]

Yes, it is possible to use the contigs generated by Minia, together with some other kind of data, to perform scaffolding.

As Minia doesn't use paired reads information, you can even used the regular paired reads used for assembly to perform scaffolding, but I would expect little gain, as insert size is small in relation to read length and there shouldn't be many gaps this size left. If you have mate-pair sequencing, then the gains in contiguity would be substantial. There is a huge number of scaffolders which use paired end / mate pairs, I don't have any particular recommendation.

There are scaffolders that use data types other than DNAseq reads to perform scaffolding, for example, proteins from a related species (PEP_scaffolder), RNAseq reads (P_RNA_scaffolder), or a closely related genome. I don't know if any of these are available to you.

Answer 2

[sebastien.letort]

Hi,

In gatb-minia-pipeline, the reads are mapped on contigs then the bam is used by Besst scaffolder.