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With current sequencing technologies, it is feasible to generate a lot of reads for a given genome. However, the assembly usually ends up in a set of contigs with gaps between them. If the sequences of one (or several) related genome(s) are already known, this information can be used to estimate the order and orientation of the contigs towards each other. This helps in the finishing phase of a sequencing project since it eases the design of specific primer sequences to fill the gaps.

comparative assembly

Description

This is a toolsuite for ordering and orienting contigs in a comparative genomic fashion. Currently two programs are included:

r2cat result r2cat, the related reference based contig arrangement tool can be used to order a set of contigs with respect to a single reference genome. This is done by mapping the contigs onto the reference using a q-gram filter. The mapping is visualized in a synteny plot.
treecat result treecat - phylogenetic tree based contig arrangement tool takes several genomes and their relationships in a phylogenetic tree into account to estimate a possible ordering of the contigs.

Sign on to this mailinglist if you want to be up to date about bugfixes and latest developments for r2cat and treecat.

Starting the application

It is easy to start the programs of this toolsuite. All that is needed is Java WebStart. To try out an application select a r2cat or treecat in navigation above.

Other tools

Here is a list of other tools which deal with the same problem of arranging contigs:

Users of CG-CAT are requested to cite :
Husemann, Peter and Stoye, Jens r2cat: synteny plots and comparative assembly, Bioinformatics, 2010