I'm a wet-lab biologist desperately trying to get to grips with some Bioinformatics.
I have some shotgun Illumina paired-end data from a gut microbiome project I'm working on. I'm considering how to go about generating contigs from reads. I've been recommended to use SPAdes which I'm reading up on at the moment.
Originally I was thinking of using FLASh however I was told it might not be suitable for metagenomic data.
My question simply is, what makes certain programs suitable for merging paired-end reads from a genome but not a metagenome? I find myself a little spoilt for choice (eg. FLASh/SPAdes/BBmap... ) with bioinformatics tools I'm always concerned I'm picking the wrong one.
Should I ideally be running my data through a couple of tools and comparing them?