Query : Pipeline [subsection]
Phylogeny Pipeline |
Pipeline  permalink |
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1 -> Alignment (ClustalW / Mafft / Muscle)
2 -> Gblocks
3 -> Phylogenetic reconstruction (Phyml / RaxML HPC MPI / MrBayes)
Under developement
MBB development Team
0.0
Pipeline - Phylogenetic reconstruction - Alignment
Assembly Pipeline |
Pipeline  permalink |
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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
1
Assembly Pipeline Paired-End data |
Pipeline  permalink |
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IDxen upload |
Alignment  permalink |
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Tool to upload new reference versions to IDxen.
Author(s)Julien Veyssier
1
Alignment - Phylogenetic reconstruction - Pipeline - Tool
Align coding sequences using MACSE (OrthoMaM pipeline)
Author(s)Vincent Ranwez
0.2.0
Dada2MetaBarcoding |
Pipeline  permalink |
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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
1
GATKsnpSeq |
Mapping  permalink |
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