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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git

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Celine Mercier
2019-09-05 17:20:13 +02:00
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@ -23,18 +23,19 @@ DNA metabarcoding offers new perspectives for biodiversity research [1]. This ap
**Tools.** The `OBITools3` offer the same tools as the original `OBITools`. Eventually, new versions of `ecoPrimers` (PCR primer design) [3], `ecoPCR` (*in silico* PCR) [4], as well as `Sumatra` (sequence alignment) and `Sumaclust` (sequence alignment and clustering) [5] will be added, taking advantage of the database structure developed for the `OBITools3`.
**Tools.** The `OBITools3` offer the same tools as the original `OBITools`, plus `ecoPCR` (*in silico* PCR) [4] and `Sumatra` (sequence alignment, not multithreaded yet) [5].
Eventually, new versions of `ecoPrimers` (PCR primer design) [3], as well as `Sumaclust` (sequence alignment and clustering) [5] will be added, taking advantage of the database structure developed for the `OBITools3`.
**Implementation and disponibility.** The lower layers managing the DMS as well as all the compute-intensive functions are coded in `C99` for efficiency reasons. A `Cython` (<http://www.cython.org>) object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3.5`. The `OBITools3` are still in development, and the first functional versions are expected for autumn 2016.
**Implementation and disponibility.** The lower layers managing the DMS as well as all the compute-intensive functions are coded in `C99` for efficiency reasons. A `Cython` (<http://www.cython.org>) object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3`. The `OBITools3` are now being released, check the wiki for more information.
**References.**
1. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH: Environmental DNA. Mol Ecol 2012:1789–1793.
2. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E: OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour 2015:n/a–n/a.
2. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E: OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour, 2016: 176-182.
3. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E: ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 2011, 39:e145.
4. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Pompanon F: An in silico approach for the evaluation of DNA barcodes. BMC Genomics 2010, 11:434.
5. Mercier C, Boyer F, Bonin A, Coissac E (2013) SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Available: <http://metabarcoding.org/sumatra> and <http://metabarcoding.org/sumaclust>