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
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
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