We have done scaffolding after de novo assembly, how to fill gap in between scaffold length and closely homolog sequence length ?
We have data of yeast (Yarrowia)sequenced using Illumina paired-end. Each read R1 and R2 has ~41 million reads. Read length is 150 and insert size is 300. I have used velvet for de novo assembly. The highest value of N50: 22726 was obtained for Kmer 93. Total contigs are ~1900. Scaffolding was done using Contiguator. Gapfiller was used to fill the gaps. Closest Yarrowia homolog has a length of ~ 20MB. Using our data I got after gapfilling ~17MB. How to fill the gap of 3MB ? Eagerly awaiting your inputs
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To close gaps you normally need to go back in the lab - PCRing junctions to work out which contigs adjoin one another and to find the missing sequence regions.
Another option is hybrid assembly with a long read technology such as pacbio or Oxford Nanopore