Fast-Plast¶
Description¶
Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and verify whole chloroplast genome sequences. For most datasets with sufficient data, Fast-Plast is able to produce a full-length de novo chloroplast genome assembly in approximately 30 minutes with no user mediation. In addition to a chloroplast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.
Environment Modules¶
Run module spider fast-plast to find out what environment modules are available for this application.
Environment Variables¶
- HPC_FASTPLAST_DIR - installation directory
- HPC_FASTPLAST_BIN - executable directory
Citation¶
If you publish research that uses fast-plast you have to cite it as follows:
Bankevich, A., S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin, A. S. Kulikov, V. M. Lesin, S. I. Niklenko, S. Pham, A. D. Prjibelski, A. V. Pyshkin, A. V. Sirotkin, N. Vyahhi, G. Tesler, M.A. Alexkseyev, and P. A. Pevzner. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comp. Biol., 19(5):455-477.
Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.
Langmead, B. and S. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9:357-359. Marçais, G. and C. Kingsford. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27:764-770.
Categories¶
biology, phylogenetics