RITA - Revision history

Beiko: /* Rapid identification of taxonomic assignments (RITA) */

2012-04-04T11:18:32Z

Rapid identification of taxonomic assignments (RITA)

2012-04-04T11:17:54Z

2012-03-06T17:32:39Z

Rank-flexible setup

2012-03-06T17:32:05Z

Rank-flexible setup

2012-03-06T17:31:22Z

Rank-flexible setup

2012-03-06T17:30:59Z

Rank-flexible setup

2012-03-06T17:30:45Z

Rank-flexible setup

2012-03-06T17:30:22Z

Rank-flexible setup

2012-03-06T17:05:48Z

Rank-flexible example usage

2012-03-06T17:04:21Z

Rank-flexible setup

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-== Rapid identification of taxonomic assignments (RITA) ==
+== Overview of RITA ==
 RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike other hybrid approaches which combine these predictions for all sequences to be classified, RITA uses a pipeline to first identify cases where both types of classifier are in agreement, which constitute the highest-confidence set. Sequences not classified in this manner are subjected to a series of downstream classification steps.
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 This work has been accepted for publication:
-MacDonald NJ, Parks DH, and Beiko RG.  Rapid identification of taxonomic assignments. Accepted to 'Nucleic Acids Research' April 4, 2012.
+MacDonald NJ, Parks DH, and Beiko RG.  Rapid identification of taxonomic assignments. Accepted to ''Nucleic Acids Research'' April 4, 2012.
 If you have any questions or bug reports, please let us know at <beiko@cs.dal.ca>.

@@ Line 1: / Line 1: @@
 == Rapid identification of taxonomic assignments (RITA) ==
-This program executes and combines the results of several BLAST algorithms with those produced
+RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike other hybrid approaches which combine these predictions for all sequences to be classified, RITA uses a pipeline to first identify cases where both types of classifier are in agreement, which constitute the highest-confidence set. Sequences not classified in this manner are subjected to a series of downstream classification steps.
-This work has been submitted for publication:
+This work has been accepted for publication:
-MacDonald NJ, Parks DH, and Beiko RG.  Rapid identification of taxonomic assignments. Submitted 2011.
+MacDonald NJ, Parks DH, and Beiko RG.  Rapid identification of taxonomic assignments. Accepted to 'Nucleic Acids Research' April 4, 2012.
 If you have any questions or bug reports, please let us know at <beiko@cs.dal.ca>.

@@ Line 118: / Line 118: @@
 * Update the MOTHUR_16S_ALIGNMENT setting in ''globalsettings.cfg'' to point to the file ''sequences_of_16s.align'' which will be in the ''rita'' directory.
-You can now use rank-flexible RITA.
+You are now ready to use rank-flexible RITA.
 == Rank-flexible example usage ==

@@ Line 114: / Line 114: @@
    mothur > align.seqs(candidate=sequences_of_16s.fasta, template=core_set_aligned.imputed.fasta, flip=t)
    mothur > quit()
-* Place a copy of the [http://www.mothur.org/wiki/Lane_mask 1349 character Lane Mask] in your MOTHUR directory.
+* Place a copy of the [http://www.mothur.org/wiki/Lane_mask 1349 character Lane Mask] in your ''mothur'' directory.
 ** Note: core_set_aligned.imputed.fasta can be obtained from the MOTHUR [http://www.mothur.org/wiki/Greengenes-formatted_databases here].
-* Update the MOTHUR_16S_ALIGNMENT setting in ''globalsettings.cfg'' to point to the file ''sequences_of_16s.align''
+* Update the MOTHUR_16S_ALIGNMENT setting in ''globalsettings.cfg'' to point to the file ''sequences_of_16s.align'' which will be in the ''rita'' directory.
 You can now use rank-flexible RITA.

@@ Line 114: / Line 114: @@
    mothur > align.seqs(candidate=sequences_of_16s.fasta, template=core_set_aligned.imputed.fasta, flip=t)
    mothur > quit()
-* Place a copy of the [http://www.mothur.org/wiki/Lane_mask lane1349.gg.filter 1349 character Lane Mask] in your MOTHUR directory.
+* Place a copy of the [http://www.mothur.org/wiki/Lane_mask 1349 character Lane Mask] in your MOTHUR directory.
 ** Note: core_set_aligned.imputed.fasta can be obtained from the MOTHUR [http://www.mothur.org/wiki/Greengenes-formatted_databases here].
 * Update the MOTHUR_16S_ALIGNMENT setting in ''globalsettings.cfg'' to point to the file ''sequences_of_16s.align''

@@ Line 120: / Line 120: @@
 == Rank-flexible example usage ==
-To run rank-flexible RITA, you must first generate a proxy file:
+To run rank-flexible RITA, you must first generate a proxy file for the 16S sequences contained in your sample:
    python rita.py --buildproxy <sample_16s_fragments.fasta> --out proxy.txt

@@ Line 89: / Line 89: @@
 == Rank-flexible setup ==
-Prerequisites:
+''Prerequisites'':
 * Install [http://biopython.org/wiki/Biopython BioPython] (needed for tree manipulation).
 * Install [http://www.mothur.org/ MOTHUR] for 16S DNA alignments.