Results

1 -> Alignment (ClustalW / Mafft / Muscle)
2 -> Gblocks
3 -> Phylogenetic reconstruction (Phyml / RaxML HPC MPI / MrBayes)
Under developement

Author(s)

MBB development Team

Version

0.0

Subsections

Pipeline - Phylogenetic reconstruction - Alignment

After read cleaning this pipeline will call Abyss for denovo assembly in contigs. The resulting contigs can be further assembled with CAP3. The contigs are then blasted against a provided multi-fasta file and/or ncbi databases. If a blastx on nr is chosen the result can be used to annotate the best hits with blast2go.

Author(s)

MBB dev

Version

1

Subsections

Pipeline - Blast - Assembler

Tags

De novo

AAA sssss aaa

Author(s)

Khalid

Version

1

Subsections

Pipeline - Assembler

Tags

De novo

IDxen : EPA on mitochondrial reads.

Author(s)

Julien Veyssier

Version

1

Subsections

Pipeline - Tool

Tool to upload new reference versions to IDxen.

Author(s)

Julien Veyssier

Version

1

Subsections

Alignment - Phylogenetic reconstruction - Pipeline - Tool

Align coding sequences using MACSE (OrthoMaM pipeline)

Author(s)

Vincent Ranwez

Version

0.2.0

Subsections

Pipeline - Alignment

Tags

Apps

The pipeline will use Dada2 package to product an amplicon sequence variant (ASV) table ( an analogue of the traditional OTU table), which records for each sample the number of times each exact amplicon sequence variant was observed.
For 16S/18S amplicon sequencing, taxonomy is assigned to these sequence variants by comparison to a training set of reference sequences with known taxonomy (from RDP, Greengenes or SILVA databases).
The alpha-diversity plot and the top20 distribution of family levels are then ploted with phyloseq package

Author(s)

M. Massaviol, K. Belkhir and E. Desmarais

Version

1

Subsections

Pipeline

A pipeline to map reads to a reference and call snp with GATK tools.

Author(s)

M. Massaviol & K. Belkhir

Version

1

Subsections

Mapping - Pipeline