From f8cccebe193cad9cc744840ce51d220e593c6d28 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Wed, 4 Sep 2019 17:11:46 +0200 Subject: [PATCH 1/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7bacb77..37828e8 100755 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ DNA metabarcoding offers new perspectives for biodiversity research [1]. This ap -**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` () 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` () object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3.5`. The `OBITools3` are now being released, check the wiki for more information. From ec614e5d151a1a9ecbaaaeb2fbcb1c8564e03233 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Wed, 4 Sep 2019 17:23:30 +0200 Subject: [PATCH 2/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 37828e8..f1c8f2c 100755 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ DNA metabarcoding offers new perspectives for biodiversity research [1]. This ap **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: and From 8899478237489705a4836bfcf38ef59026d31c7c Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Wed, 4 Sep 2019 17:29:45 +0200 Subject: [PATCH 3/3] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f1c8f2c..17c57ab 100755 --- a/README.md +++ b/README.md @@ -23,11 +23,12 @@ 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` () object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3.5`. The `OBITools3` are now being released, check the wiki for more information. +**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` () 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.