Commit c839b015 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

add mothur documentation

parent 7a68040b
<p>
From the <a href="http://www.mothur.org">mothur</a> web site.
</p>
<h3>inputs</h3>
<p>
<ul>
<li>input file list: the file list of files to align.</li>
<li>input file: the single file to align.</li>
<li>input directory: the directory within files to align.</li>
<li>input extension: the following is only used when iterating over an input directory.</li>
<li>ng6cfg file: the NG6 run configuration file the analysis belongs to.</li>
<li>project id: the project id the analysis belongs to. </li>
<li>database: the database to use for the alignment. </li>
<li>parent analysis file: the parent analysis config file (if this analysis was processed after an other one, provide the previous
analysis config file to keep hierarchical traceability).</li>
</ul>
</p>
<h3>outputs</h3>
<ul>
<li>aligned fasta list: the list of fasta file within aligned sequences.</li>
<li>aligned name list: the list of name file within aligned sequences.</li>
<li>group list: the list of group files.</li>
<li>analysis config file: the analysis config file (usefull to keep hierarchical traceability).</li>
</ul>
<h3>parameters</h3>
<p>
<ul>
<li>search algorithm: mothur offers three methods of finding the template sequence kmer searching, blast, and suffix tree searching,</li>
<li>kmer size: change the size of kmers that are used in align.seqs,</li>
<li>alignment method: the align.seqs command allows you to select between three alignment methods blastn, gotoh, and needleman,</li>
<li>match: in the pairwise alignment portion of the aligning procedure, the default reward for a match is +1,</li>
<li>mismatch: in the pairwise alignment portion of the aligning procedure, the default reward for a mismatch is -1,</li>
<li>gapopen: in the pairwise alignment portion of the aligning procedure, the default reward for a gap opening is -2,</li>
<li>gapextends: in the pairwise alignment portion of the aligning procedure, the default reward for a gap extension is -1,</li>
<li>threshold: the threshold parameter is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried,</li>
<li>flip: flip sequences before to align,</li>
<li>processors: the processors option enables you to accelerate the alignment by using multiple processors.,</li>
<li>use file as sample: should files be computed together (as samples) or independently,</li>
<li>analysis name: the analysis name to display in ng6,</li>
<li>analysis description: the analysis description to display in ng6,</li>
<li>results archive name: the results archive name to display in ng6.</li>
</ul>
</p>
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<p>
From the <a href="http://www.mothur.org">mothur</a> web site.
</p>
<h3>inputs</h3>
<p>
<ul>
<li>input file list: the file list of files to classify.</li>
<li>input file: the single file to classify.</li>
<li>input directory: the directory within files to classify.</li>
<li>input extension: the following is only used when iterating over an input directory.</li>
<li>name file list: the name files list outputed by mothur_align.</li>
<li>group file list: the group files list outputed by mothur_align.</li>
<li>ng6cfg file: the NG6 run configuration file the analysis belongs to.</li>
<li>project id: the project id the analysis belongs to. </li>
<li>template file: the taxonomic template file. </li>
<li>taxonomy file: the taxonomy file. </li>
<li>parent analysis file: the parent analysis config file (if this analysis was processed after an other one, provide the previous
analysis config file to keep hierarchical traceability).</li>
</ul>
</p>
<h3>outputs</h3>
<ul>
<li>taxonomy result list: the list of taxonomy files.</li>
<li>summary list: the list of summary files.</li>
<li>analysis config file: the analysis config file (usefull to keep hierarchical traceability).</li>
</ul>
<h3>parameters</h3>
<p>
<ul>
<li>analysis name: the analysis name to display in ng6,</li>
<li>analysis description: the analysis description to display in ng6,</li>
<li>results archive name: the results archive name to display in ng6.</li>
</ul>
</p>
\ No newline at end of file
<p>
From the <a href="http://www.mothur.org">mothur</a> web site.
</p>
<h3>inputs</h3>
<p>
<ul>
<li>input file list: the file list of files to classify.</li>
<li>input file: the single file to classify.</li>
<li>input directory: the directory within files to classify.</li>
<li>input extension: the following is only used when iterating over an input directory.</li>
<li>name file list: the name files list outputed by mothur_align.</li>
<li>group file list: the group files list outputed by mothur_align.</li>
<li>ng6cfg file: the NG6 run configuration file the analysis belongs to.</li>
<li>project id: the project id the analysis belongs to. </li>
<li>parent analysis file: the parent analysis config file (if this analysis was processed after an other one, provide the previous
analysis config file to keep hierarchical traceability).</li>
</ul>
</p>
<h3>outputs</h3>
<ul>
<li>analysis config file: the analysis config file (usefull to keep hierarchical traceability).</li>
</ul>
<h3>parameters</h3>
<p>
<ul>
<li>calc: mothur has several ways of calculating a distance based on how gaps are treated onegap|nogaps|eachgap,</li>
<li>countends: ideally, all sequences would be aligned over the same region; however, if this is; not possible or desired for some reason the ends option can be employed to tell; mothur to ignore the penalization. ,</li>
<li>cluster method: clustering method to use to clusterize sequences average|nearest|furthest,</li>
<li>shared label: there may only be a couple of lines in your OTU data that you are interested in summarizing,</li>
<li>processors: the processors option enables you to accelerate the alignment by using multiple processors,</li>
<li>analysis name: the analysis name to display in ng6,</li>
<li>analysis description: the analysis description to display in ng6,</li>
<li>results archive name: the results archive name to display in ng6.</li>
</ul>
</p>
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