Published June 21, 2014
| Version v1
Poster
Open
ChloroExtractor: A fully automated plastid assembly pipeline reveals dozens of novel plastid genomes
- 1. Massachusetts Institute of Technology, Department of Civil and Environmental Engineering
- 2. University of Wuerzburg, Department of Animal Ecology and Tropical Biology
- 3. University of Wuerzburg, Department of Plant Physiology and Biophysics
- 4. University of Wuerzburg, Department of Bioinformatics
Description
In times of large scale high troughput sequencing, novel plastid genomes mostly emerge from host genome sequencing projects. Here we present ChloroExtractor, a fully automated pipeline designed to generate high quality plastid assemblies from heterogeneous short read data. By applying our software to 100 publicly available plant sequencing libraries, we salvaged 27 novel and complete plastid genomes across a wide range of plant taxa. Thus, we consider ChloroExtractor a valuable tool in the process of further unraveling plastid biology and evolution.
Files
ChloroExtractor-poster-90dpi.pdf
Files
(1.4 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:3a1b4670a19829e6d6de442de44827a9
|
1.4 MB | Preview Download |
Additional details
Related works
- Is identical to
- 10.13140/RG.2.1.1331.6328 (DOI)
References
- Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods
- Marçais, G., & Kingsford, C. (2011). A fast, lock-free approach for e ffi cient parallel counting of occurrences of k-mers. Bioinformatics (Oxford, England), 27, 764–770
- Zerbino, D. R., & Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18, 821–829
- Green, P. (2009). Phrap, version 1.090518. Retrieved from http://phrap.org
- Liu, C., Shi, L., Zhu, Y., Chen, H., Zhang, J., Lin, X., & Guan, X. (2012). CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics, 13, 715
- Lohse, M., Drechsel, O., & Bock, R. (2007). OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics, 52(5-6), 267–7 4