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DefaultPipelines

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Schloss_SOP

The GUI comes with the Schloss SOP already set for you to use. You can load a pipeline by clicking on the name. You can run the SOP with Pat's example files or go through the commands inserting your own files.

DefaultPipelines.jpg


Reducing_Sequencing_Errors

The Reducing_Sequencing_Errors pipeline includes the trim.flows, shhh.flows, trim.seqs and summary.seqs commands.

ReducingSeqErrors.jpg

Processing_Improved_Sequences

The Processing_Improved_Sequences pipeline includes the unique.seqs, summary.seqs, align.seqs, screen.seqs, filter.seqs and pre.cluster commands.

ProcessingImprovedSeqs.jpg

Remmoving_Chimeras

The Remmoving_Chimeras pipeline includes the chimera.uchime, remove.seqs and summary.seqs commands.

RemovingChimeras.jpg

Removing_Contaminants

The Remmoving_Chimeras pipeline includes the classify.seqs, remove.lineage and summary.seqs commands.

RemovingContaminants.jpg

Preparing_Inputs_For_Analysis

The Preparing_Inputs_For_Analysis pipeline includes the dist.seqs, cluster, make.shared, count.groups, sub.sample, classify.otu, phylotype, clearcut commands.

PreparingInputs.jpg

Error_Analysis

The Error_Analysis pipeline includes the filter.seqs, get.groups, seq.error, get.seqs, dist.seqs, cluster, summary.single commands.

ErrorAnalysis.jpg

Analysis

The Analysis pipeline includes the collect.single, rarefaction.single, catchall, summary.single, heatmap.bin, heatmap.sim, venn, summary.shared, tree.shared, parsimony, unifrac.weighted, unifrac.unweighted, dist.shared, pcoa, nmds, amova, corr.axes, metastats and phylo.diversity.

Analysis.jpg