Difference between revisions of "Fast-Plast"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
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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. | 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. | ||
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Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. | Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. | ||
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Langmead, B. and S. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9:357-359. | 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. | Marçais, G. and C. Kingsford. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27:764-770. | ||
Latest revision as of 21:20, 6 December 2019
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.
Currently, Fast-Plast is written to accomodate Illumina data, although most data types could be used.
Fast-Plast uses a de novo assembly approach by combining the De Bruijn graph-based method of SPAdes with an iterative seed-based assembly implemented in afin to close gaps of contigs with low coverage. The pipeline then identifies regions from the quadripartite structure of the chloroplast genome, assigns identity, and orders them according to standard convention. A coverage analysis is then conducted to assess the quality of the final assembly.
Environment Modules
Run module spider fast-plast to find out what environment modules are available for this application.
System Variables
- HPC_FAST-PLAST_DIR - installation directory
- HPC_FAST-PLAST_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.