Online tools

Results

Query : Pipeline [subsection]

Online Tools (15)

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

Pipeline

 

IDxen : EPA on mitochondrial reads.

Author(s)

Julien Veyssier


Version

1


Subsections

Pipeline - Tool


IDxen upload

Alignment

 

Tool to upload new reference versions to IDxen.

Author(s)

Julien Veyssier


Version

1


Subsections

Alignment - Phylogenetic reconstruction - Pipeline - Tool


OMM_MACSE

Pipeline

 

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


GATKsnpSeq

Mapping

 

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