Pipelines and ready-to-use database for metabarcoding

Ready to use libraries for metabarcoding pipelines are available for rbcL: 

• For DADA2:
  • v15 : "A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2", https://doi.org/10.57745/SE6GJH
  • v14 : A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2", https://doi.org/10.57745/SE6GJH
  • v12 : A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v12", https://doi.org/10.57745/XWJJGI 
  • v10 : developped from Diat.barcode version 10 : A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v10
  • v9 : developped from Diat.barcode version 9 : A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v9
  • v7 : developped from Diat.barcode version 7: A ready-to-use database for DADA2: Diat.barcode_rbcL_312bp_DADA2
• DADA2 ready to use pipeline available at: https://github.com/fkeck/DADA2_diatoms_pipeline

• For MOTHUR:
  • developped from Diat.barcode version 10 : A ready-to-use database for mothur: Diat.barcode_rbcL_263bp_mothur based on Diat.barcode v10
  • developped from Diat.barcode version 9: Chonova, Teofana; Vasselon, Valentin; Bouchez, Agnès; Rimet, Frédéric, 2020, "A ready-to-use database for mothur: Diat.barcode_rbcL_263bp_mothur based on Diat.barcode v9", https://doi.org/10.15454/SOMFSU, Portail Data INRAE, V1
  • developped from Diat.barcode version 7: Rsyst::diatom_rbcl_align_312bp database: a database adapted to DNA metabarcoding
  • Citation: Vasselon, Valentin; Rimet, Frederic; Bouchez, Agnès, 2018, "Rsyst::diatom_rbcl_align_312bp database: a database adapted to DNA metabarcoding (version v7: 23-02-2018)", https://doi.org/10.15454/HYRVUH, Portail Data Inra, V1

• For FROGS:
  • FROGS maybe used on Galaxy interface or in command line
  • the formated Diat.barcode v10.1 is available at http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/Diat.barcode/ 
  • All rbcl sequences have been taken into account without any primer trimming or sequence dereplication. This allow FROGS to return all equivalent affiliation during metabarcoding analysis. Taxonomies returned are the most commonly used one and are defined on 9 ranks. Sequences have then been formatted/indexed for RDP classifier, and NCBI Blast+ (Script and procedure to format Diat.barcode database are downloadable at the bottom of this page)
  • FROGS publication: https://academic.oup.com/bioinformatics/article/34/8/1287/4708232
  • All rbcl sequences have been taken into account without any primer trimming or sequence dereplication. This allow FROGS to return all equivalent affiliation during metabarcoding analysis. Taxonomies returned are the most commonly used one and are defined on 9 ranks. Sequences have then been formatted/indexed for RDP classifier, and NCBI Blast+.

• Curation procedure details of the ready to use libraries for metabarcoding are given in the files below: