Genome Gap Closing/Finishing Software

[akjones]

Hi all,

I am working with the genome of a Gram- bacterium, ~3.6Mb. The genome was sequenced using an Illumina MiSeq platform with paired-end reads and a de novo assembly was done using CLC Genomics Workbench. Further assembly of scaffolds was done using Geneious, since it allowed for better visualization of large scaffolds. I am now left with some ambiguous gaps in the genome as a result of the scaffolding process. Does anyone have a particular gap closing software that they would recommend from experience? I am working with Mac OSX as an operating system and my command-line experience is minimal (pretty much limited to local blasting and CD hit).

Thanks very much

[cistronic]

Since you are using the CLC Genomics Workbench, you might want to check out their MICROBIAL GENOME FINISHING MODULE
http://www.clcbio.com/clc-plugin/gen...ishing-module/
A new updated version has recently been released, see
http://www.clcbio.com/news/clc-bio-r...ome-finishing/

[GenoMax]

Since you are using the CLC Genomics Workbench, you might want to check out their MICROBIAL GENOME FINISHING MODULE
http://www.clcbio.com/clc-plugin/gen...ishing-module/
A new updated version has recently been released, see
http://www.clcbio.com/news/clc-bio-r...ome-finishing/

As a fair warning that module requires a separate license (that is what I remember from previous discussion with CLC).