I am teaching a Genomics Biotechnology class this semester at UNC Charlotte and have a question about the best alignment tool to use for a class project.
Students in the class are using Ion Torrent PGM to sequence the chloroplast genomes of several different cultivars of tomato. The students made libraries by amplifying chloroplast DNA (using long-range PCR), fragmenting the amplicons, ligating adapters, and then amplifying the libraries. In the next week, they'll sequence their libraries on the Ion Torrent PGM.
We have a tomato chloroplast reference sequence and would like to align the students' reads onto the reference. Recall that the chloroplast genome is circular.
Ion Torrent is prone to introducing lots of deletions and insertions next to runs of the same base. The data seem very similar to 454 data in that respect.
My question for you is:
- What alignment tool would you recommend we use?
We aligned data from previous years classes onto a reference chloroplast genome using bowtie2, but probably there are other tools that would work just as well, or even better.
Data from previous years classes are available in Integrated Genome Browser if you want to take a look. To see the data in IGB:
- Start IGB (go to bioviz.org to get a copy)
- Click the tomato shortcut image (on the left side of the Mona Lisa image, past rice and Arabidopsis)
- Select the chloroplast genome (in Current Sequence tab)
- Open and view data files in the folder named "Plastid Re-sequencing" (in Available Data section of the Data Access tab