I have metagenomic Illumina data (HiSeq 101b reads- one paired-end, one 180b overlapped paired-end and two mate-pair (2-5k) lib). Can someone suggest/describe the best approach or a pipeline to do denovo assembly?
Thanks for all the suggestion. yes it is whole-genome "shotgun" metagenomic data from Illumina with 101bp paired reads. i have three libraries 1. 180bp overlapped paired library, 2. 2K mate-pair library, 3. 5K mate-pair library
I appreciate your suggestion