fixes the errors!

jwdebelius · Jan 4, 2021 · 0febec9 · 0febec9
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diff --git a/docs/source/database_preparation.rst b/docs/source/database_preparation.rst
@@ -277,10 +277,12 @@ Database References
 .. _filtering by taxonomy: https://docs.qiime2.org/2020.6/tutorials/filtering/#taxonomy-based-filtering-of-tables-and-sequences
 .. _qiime filtering tutorial: https://docs.qiime2.org/2020.6/tutorials/filtering/#taxonomy-based-filtering-of-tables-and-sequences
 .. _qiime feature classifier: https://docs.qiime2.org/2020.6/tutorials/feature-classifier/#extract-reference-reads
+.. _feature classifier: https://docs.qiime2.org/2020.6/tutorials/feature-classifier/#extract-reference-reads
 .. _qiime2 view : https://view.qiime2.org
 
 .. citations
 
 .. [1] Fuks, C; Elgart, M; Amir, A; et al (2018) "Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling." *Microbiome*. **6**:17. doi: 10.1186/s40168-017-0396-x
 .. [2] McDonald, D; Price, NM; Goodrich, J, et al (2012). "An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea." *ISME J*. **6**: 610. doi: 10.1038/ismej.2011.139
 .. [3] Quast, C.; Pruesse, E; Yilmaz, P; et al. (2013) "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools." *Nucleic Acids Research*. **41**:D560. doi: 10.1093/nar/gks1219
+.. [4] Michael S Robeson II, Devon R O'Rourke, Benjamin D Kaehler, et al. "RESCRIPt: Reproducible sequence taxonomy reference database management for the masses."" bioRxiv 2020.10.05.326504; doi: 10.1101/2020.10.05.326504
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -14,8 +14,8 @@ Sidle is a python version of the Short MUliple Reads Framework (SMURF) algorithm
 	:caption: Contents:
 
 	install
-	database_preperation
-	read_preperation
+	database_preparation
+	read_preparation
 	reconstruction
 	parallel_processing
 

diff --git a/docs/source/read_preparation.rst b/docs/source/read_preparation.rst
@@ -60,7 +60,7 @@ If your samples are demultiplexed to include a single set of files (probably for
 This will give you a table per region. Next, continue on to `denoise the regions`_.
 
 .. _trimming your primers:
-.. _demultiplex by sample and region:
+.. _demultiplexed correctly:
 
 Sequences barcoded by sample and region
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -255,7 +255,6 @@ Read Preparation References
 .. _q2 cutadapt: https://docs.qiime2.org/2020.6/plugins/available/cutadapt/
 .. _cutadapt: https://cutadapt.readthedocs.io/en/stable/
 .. _filter your sequences: https://docs.qiime2.org/2020.2/plugins/available/demux/filter-samples/
-.. _denoise the regions: _denoising
 .. _Dada2: https://docs.qiime2.org/2020.6/plugins/available/dada2/
 .. _Deblur: https://docs.qiime2.org/2020.6/plugins/available/deblur/
 .. _Nearing et al: https://peerj.com/articles/5364/
@@ -269,5 +268,6 @@ Read Preparation References
 .. _moving pictures option 2: https://docs.qiime2.org/2020.6/tutorials/moving-pictures/#option-2-deblur
 .. _Atacama Soils: https://docs.qiime2.org/2020.6/tutorials/atacama-soils/#paired-end-read-analysis-commands
 .. _alternative methods of read joining: https://docs.qiime2.org/2020.6/tutorials/read-joining/
-
+.. _rename the sample ids: https://docs.qiime2.org/2020.11/plugins/available/feature-table/rename-ids/
+.. _rename your samples: https://docs.qiime2.org/2020.11/plugins/available/feature-table/rename-ids/