I have Single End Illumina reads with read length around 76bp; and probably around 30X coverge for the Drosophila related species. After Quality filtering the Reads, I am trying denovo assembly with Abyss and IDBA assemblers, Got contigs with N50 length of around 800 to 1200 bp depending on the K-mer value used (25-60) (Is it terrible?). I am facing difficulty to build super-contigs (scaffolds) since I do not have Paired end information as they are SE. Suggest me with possible denovo assembly pipeline(s) to build scaffolds with SE data in hand.
Treat it as follow up of the previous Question assked in the Biostar