Hi, everyone. I obtained the contigs of a genome of NCBI (of 454 sequencing) and I want to improve the coverage of this genome sequenced, for this I obtain the genome sequencing using illumina (pair-end). I would like to map the reads generated in Illumina in the contigs and improve the coverage of this genome. In mira, Can I use contigs Instead of reads? Because I'don t have the reads of 454 in fastq format. Please, Thank you for any help.

Here's a paper: https://www.ncbi.nlm.nih.gov/pubmed/22750884

Abstract Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.