Fungal genome de novo assembly and scaffolding

neerajbharti · 05-04-2017, 01:49 AM

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

Brian Bushnell · 05-04-2017, 10:20 AM

I suggest you try assembling with Spades; it often yields better continuity than Velvet.

WhatsOEver · 05-05-2017, 12:14 AM

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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05-04-2017, 01:49 AM	#1
neerajbharti Junior Member Location: India Join Date: Dec 2011 Posts: 1	Fungal genome de novo assembly and scaffolding 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

05-04-2017, 10:20 AM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	I suggest you try assembling with Spades; it often yields better continuity than Velvet.

05-05-2017, 12:14 AM	#3
WhatsOEver Senior Member Location: Germany Join Date: Apr 2012 Posts: 215	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