I'm looking to make some proposals for QC pipelines for a range of sequencing applications. Two of the applications I'm thinking about are genome sequencing and transcriptome sequencing. When a reference is not available, a quick and dirty assembly is desirable to map reads to.
I wondered if anyone knows of any assembler which contains modules for doing both genomic and transcriptomic de novo assembly. This would be desirable as I could then recommend using a single assembler for reference-free QC of both applications, with an option set to indicate which type of assembly is desired. I've not been able to find anything by googling.
I appreciate that this is very unlikely given the disparities between the characteristics of the two types of data. To make matters worse, I'm looking for something which produces decent results quickly (i.e. not something which is liable to hold up QC by taking days to run). The assembly doesn't need to be perfect or even particularly good, it just needs to be good enough to allow confidence in looking at things like % of reads which map to contigs. Freely-available software would be a massive bonus.