Hello,
I have just started working on viral genome mapping using Geneious. I did De Novo assembly of raw reads and then performed blast search of the contigs from De Novo. I got the longest contig matches with one of the reference sequence of the same virus species. Using this sequence as a reference, I tried to align the raw reads. What I found that half of the reads overlapped on the ref sequence and several contigs extend beyond the reference sequence. At the same time there are gaps between the aligned contigs and I did not get the expected length of the genome.
There are always some gaps between the contigs, and if you can't fill the gaps, maybe you can try do another library sequence with more depth or just simply design primers based on current contigs to fill the gaps.
I agree with Yanpeng Li, you need to prepare more individual cDNA libraries with higher sequencing depth, or perform PCR and Sanger sequencing with specific primers designed based on the obtained contigs.
- Badges
- Science topic
- Similar topics
- Biological Science
- Microbiology
- Virology
- Virus