I’d like to incorporate some short-read genome assembly programs into Galaxy. The Velvet assembler is a particular favourite of our facility and ideally I would like to give our users the option of running Velvet assemblies on FASTQ datasets. The ideal scenario would be for the contigs generated by velvet to then be piped into an interface to interproscan.

However, in the first instance, I’d like to focus on the velvet interface. My main question centres around whether the format velvet uses to store information is representable as a composite datatype in Galaxy.

Velvet comprises of two elements – a prep step (velveth) followed by the actual assembly (velvetg). Velveth generates a directory with files (the files always have the same names). Velvetg is then run with the directory containing the relevant files as a parameter.

I have read through the composite datatypes wiki page but I’m not sure if this form of data storage can be represented in galaxy at the moment.

Any advice would be much appreciated.

All the very best,

Konrad.

Dr Konrad Paszkiewicz

Exeter Sequencing Service,

Biosciences,

Stocker Road,

University of Exeter,

Exeter EX4 4QD, UK.

http://biosciences.exeter.ac.uk/facilities/sequencing/