reassembly of contig into scaffolds

Question

[v.k17491]

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...

Answer 1

[Sej Modha]

For reference guided assembly you can use idba-ud.