Question: reassembly of contig into scaffolds
1
gravatar for v.k17491
4.7 years ago by
v.k1749110
v.k1749110 wrote:

Hello!! I have assembled 22MB fungal genome into contigs through velvet-denovo assembler. I got no. of contigs and N50, 1700 & 25K respectively. Now I want to do reference guided reassembly of contigs. So with NUCmer, i aligned the contigs (fastq format) to reference (fasta format). then provide aligned BAM file to velvet with Contig and reference genome. But velvet is giving error i.e.: velvet cann't accept refrence fasta file and K-mer is very low

NCBI has only fasta file of reference genome.

please help me out...

assembly • 1.7k views
ADD COMMENTlink modified 4.7 years ago by Sej Modha4.8k • written 4.7 years ago by v.k1749110
1
gravatar for Sej Modha
4.7 years ago by
Sej Modha4.8k
Glasgow, UK
Sej Modha4.8k wrote:

For reference guided assembly you can use idba-ud.

ADD COMMENTlink written 4.7 years ago by Sej Modha4.8k
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