Hi all,
I'm wondering if anyone has experience in duplication of contigs for the final stitching of a denovo assembly of a bacterial genome?
I've done a 454/Illumina hybrid assembly in MIRA and am now trying to reduce the number of contigs by stitching contigs together manually. I have a decent reference genome (190 contigs for a 7Mbp genome) so I know where some of the 16S RNA repetitive regions should be to join some of the larger contigs. The problem I run into is when I join a non-repetitive contig to a repetitive one there is only one copy of the repetitive contig even though it should be represented in the genome 4-5 times (I'm using GAP5 to do this). Is there a way to duplicate these contigs so I can assemble them more than once and hence stitch the genome together better?
Thanks
Derek
I'm wondering if anyone has experience in duplication of contigs for the final stitching of a denovo assembly of a bacterial genome?
I've done a 454/Illumina hybrid assembly in MIRA and am now trying to reduce the number of contigs by stitching contigs together manually. I have a decent reference genome (190 contigs for a 7Mbp genome) so I know where some of the 16S RNA repetitive regions should be to join some of the larger contigs. The problem I run into is when I join a non-repetitive contig to a repetitive one there is only one copy of the repetitive contig even though it should be represented in the genome 4-5 times (I'm using GAP5 to do this). Is there a way to duplicate these contigs so I can assemble them more than once and hence stitch the genome together better?
Thanks

Derek
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