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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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I suggest you try assembling with Spades; it often yields better continuity than Velvet. -
Why do you expect the genomes to have the exact same sizes? "Closest" sequenced homolog can still be far far away. I would say you go for more meaningful assembly quality assessment criteria.
Alternatively, you could just randomly try assemblers until you find one that gives you ~20MB
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