Tool:Contiguator: A Bacterial Genomes Finishing Tool For Structural Insights On Draft Genomes

Question

[mgalactus]

CONTIGuator is a Python script whose purpose is to speed-up the bacterial genome finishing process and to obtain a first insight of the genome structure using the artemis comparison tool (ACT), as well as gap-closing PCR primers using primer3. The program can be used using rerence genomes with more than one replicon.

Features

• Blast-based scaffolding
• Detailed information on the position of the contigs on the reference genome
• Synthenyc and non-synthenyc regions are highlighted
• Putative contigs overlap are highlighted
• Interactive ACT maps
• Publication-quality PDF maps
• Generation of gap-closing PCR primers

Online version

From the project website there's a link to the CONTIGuator web server

Code

The source code can be found at github

Documentation

The project website contains a section with the explanation of the workflow and program's parameters, as well as examples

[Istvan Albert]

The site looks awesome, makes me want to use the tool - nice job!

PS. the title is a bit hard to read

[mgalactus]

The magic of twitter bootstrap :)

Answer 1

[div]

Hi mgalactus,

I am divya, I'm also working on bacterial genome it is from S. aureus strains. Now they are in contig stage my aim is to uplift these draft genome to chromosome level. Is this tool suitable for my strains to achieve my goals.

[mgalactus]

Hi div,

yes, CONTIGuator should be able to help you with that, granted that you have a closed reference genome (which should be the case for S. aureus). You also might want to try a new multiple genomes scaffolder called Medusa, which uses more than one reference genome to scaffold the contigs.