I have some questions for my Whole Genome Sequences on Illumina Miseq (150bp; paired-end) platform. Since the size of Illumina Miseq was 150bp, I have a lot of reads in raw fastq files. I trimmed the sequence based on the Phred score, quality, and sequence length, and assembled with Abyss, but still the number of contigs is too many (13173), so I was not able to upload the contig file to Annotation server (RAST). Would you give me some suggestions that I can reduce my contig number by using Abyss or different assembly software? Your suggestions would be appreciated it. Thank you.