sync

_data/programs.yml

@@ -193,18 +193,9 @@
 - author: watsonar
   programs:
     - name: anvi-display-contigs-stats
-- author: qclayssen
-  programs:
-    - name: anvi-estimate-scg-taxonomy
-    - name: anvi-run-scg-taxonomy
-    - name: anvi-setup-scg-taxonomy
-- author: shaiberalon
-  programs:
-    - name: anvi-export-locus
-    - name: anvi-gen-variability-profile
-    - name: anvi-run-workflow
 - author: semiller10
   programs:
+    - name: anvi-draw-kegg-pathways
     - name: anvi-get-codon-frequencies
     - name: anvi-get-codon-usage-bias
     - name: anvi-get-metabolic-model-file
@@ -218,6 +209,16 @@
     - name: anvi-setup-kegg-data
     - name: anvi-setup-modelseed-database
     - name: anvi-trnaseq
+- author: qclayssen
+  programs:
+    - name: anvi-estimate-scg-taxonomy
+    - name: anvi-run-scg-taxonomy
+    - name: anvi-setup-scg-taxonomy
+- author: shaiberalon
+  programs:
+    - name: anvi-export-locus
+    - name: anvi-gen-variability-profile
+    - name: anvi-run-workflow
 - author: matthewlawrenceklein
   programs:
     - name: anvi-interactive

help/main/artifacts/bam-file/index.md

@@ -29,7 +29,7 @@ A BAM-type anvi'o artifact. This artifact is typically provided **by the user**
 ## Required or used by
 
 
-<p style="text-align: left" markdown="1"><span class="artifact-r">[anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam)</span> <span class="artifact-r">[anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene)</span> <span class="artifact-r">[anvi-get-tlen-dist-from-bam](../../programs/anvi-get-tlen-dist-from-bam)</span> <span class="artifact-r">[anvi-profile](../../programs/anvi-profile)</span> <span class="artifact-r">[anvi-profile-blitz](../../programs/anvi-profile-blitz)</span> <span class="artifact-r">[anvi-report-linkmers](../../programs/anvi-report-linkmers)</span> <span class="artifact-r">[anvi-script-find-misassemblies](../../programs/anvi-script-find-misassemblies)</span> <span class="artifact-r">[anvi-script-get-coverage-from-bam](../../programs/anvi-script-get-coverage-from-bam)</span> <span class="artifact-r">[anvi-script-reformat-bam](../../programs/anvi-script-reformat-bam)</span></p>
+<p style="text-align: left" markdown="1"><span class="artifact-r">[anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam)</span> <span class="artifact-r">[anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene)</span> <span class="artifact-r">[anvi-get-tlen-dist-from-bam](../../programs/anvi-get-tlen-dist-from-bam)</span> <span class="artifact-r">[anvi-profile-blitz](../../programs/anvi-profile-blitz)</span> <span class="artifact-r">[anvi-report-linkmers](../../programs/anvi-report-linkmers)</span> <span class="artifact-r">[anvi-script-find-misassemblies](../../programs/anvi-script-find-misassemblies)</span> <span class="artifact-r">[anvi-script-get-coverage-from-bam](../../programs/anvi-script-get-coverage-from-bam)</span> <span class="artifact-r">[anvi-script-reformat-bam](../../programs/anvi-script-reformat-bam)</span></p>
 
 
 ## Description

help/main/artifacts/contigs-db/index.md

@@ -29,7 +29,7 @@ A DB-type anvi'o artifact. This artifact is typically generated, used, and/or ex
 ## Required or used by
 
 
-<p style="text-align: left" markdown="1"><span class="artifact-r">[anvi-cluster-contigs](../../programs/anvi-cluster-contigs)</span> <span class="artifact-r">[anvi-compute-completeness](../../programs/anvi-compute-completeness)</span> <span class="artifact-r">[anvi-db-info](../../programs/anvi-db-info)</span> <span class="artifact-r">[anvi-delete-functions](../../programs/anvi-delete-functions)</span> <span class="artifact-r">[anvi-delete-hmms](../../programs/anvi-delete-hmms)</span> <span class="artifact-r">[anvi-display-contigs-stats](../../programs/anvi-display-contigs-stats)</span> <span class="artifact-r">[anvi-display-metabolism](../../programs/anvi-display-metabolism)</span> <span class="artifact-r">[anvi-display-structure](../../programs/anvi-display-structure)</span> <span class="artifact-r">[anvi-draw-kegg-pathways](../../programs/anvi-draw-kegg-pathways)</span> <span class="artifact-r">[anvi-estimate-genome-completeness](../../programs/anvi-estimate-genome-completeness)</span> <span class="artifact-r">[anvi-estimate-metabolism](../../programs/anvi-estimate-metabolism)</span> <span class="artifact-r">[anvi-estimate-scg-taxonomy](../../programs/anvi-estimate-scg-taxonomy)</span> <span class="artifact-r">[anvi-estimate-trna-taxonomy](../../programs/anvi-estimate-trna-taxonomy)</span> <span class="artifact-r">[anvi-export-contigs](../../programs/anvi-export-contigs)</span> <span class="artifact-r">[anvi-export-functions](../../programs/anvi-export-functions)</span> <span class="artifact-r">[anvi-export-gene-calls](../../programs/anvi-export-gene-calls)</span> <span class="artifact-r">[anvi-export-gene-coverage-and-detection](../../programs/anvi-export-gene-coverage-and-detection)</span> <span class="artifact-r">[anvi-export-locus](../../programs/anvi-export-locus)</span> <span class="artifact-r">[anvi-export-misc-data](../../programs/anvi-export-misc-data)</span> <span class="artifact-r">[anvi-export-splits-and-coverages](../../programs/anvi-export-splits-and-coverages)</span> <span class="artifact-r">[anvi-export-splits-taxonomy](../../programs/anvi-export-splits-taxonomy)</span> <span class="artifact-r">[anvi-gen-fixation-index-matrix](../../programs/anvi-gen-fixation-index-matrix)</span> <span class="artifact-r">[anvi-gen-gene-consensus-sequences](../../programs/anvi-gen-gene-consensus-sequences)</span> <span class="artifact-r">[anvi-gen-gene-level-stats-databases](../../programs/anvi-gen-gene-level-stats-databases)</span> <span class="artifact-r">[anvi-gen-structure-database](../../programs/anvi-gen-structure-database)</span> <span class="artifact-r">[anvi-gen-variability-profile](../../programs/anvi-gen-variability-profile)</span> <span class="artifact-r">[anvi-get-aa-counts](../../programs/anvi-get-aa-counts)</span> <span class="artifact-r">[anvi-get-codon-frequencies](../../programs/anvi-get-codon-frequencies)</span> <span class="artifact-r">[anvi-get-codon-usage-bias](../../programs/anvi-get-codon-usage-bias)</span> <span class="artifact-r">[anvi-get-metabolic-model-file](../../programs/anvi-get-metabolic-model-file)</span> <span class="artifact-r">[anvi-get-pn-ps-ratio](../../programs/anvi-get-pn-ps-ratio)</span> <span class="artifact-r">[anvi-get-sequences-for-gene-calls](../../programs/anvi-get-sequences-for-gene-calls)</span> <span class="artifact-r">[anvi-get-sequences-for-hmm-hits](../../programs/anvi-get-sequences-for-hmm-hits)</span> <span class="artifact-r">[anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam)</span> <span class="artifact-r">[anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene)</span> <span class="artifact-r">[anvi-get-split-coverages](../../programs/anvi-get-split-coverages)</span> <span class="artifact-r">[anvi-import-collection](../../programs/anvi-import-collection)</span> <span class="artifact-r">[anvi-import-functions](../../programs/anvi-import-functions)</span> <span class="artifact-r">[anvi-import-misc-data](../../programs/anvi-import-misc-data)</span> <span class="artifact-r">[anvi-import-taxonomy-for-genes](../../programs/anvi-import-taxonomy-for-genes)</span> <span class="artifact-r">[anvi-inspect](../../programs/anvi-inspect)</span> <span class="artifact-r">[anvi-interactive](../../programs/anvi-interactive)</span> <span class="artifact-r">[anvi-merge](../../programs/anvi-merge)</span> <span class="artifact-r">[anvi-migrate](../../programs/anvi-migrate)</span> <span class="artifact-r">[anvi-profile](../../programs/anvi-profile)</span> <span class="artifact-r">[anvi-profile-blitz](../../programs/anvi-profile-blitz)</span> <span class="artifact-r">[anvi-reaction-network](../../programs/anvi-reaction-network)</span> <span class="artifact-r">[anvi-refine](../../programs/anvi-refine)</span> <span class="artifact-r">[anvi-rename-bins](../../programs/anvi-rename-bins)</span> <span class="artifact-r">[anvi-run-cazymes](../../programs/anvi-run-cazymes)</span> <span class="artifact-r">[anvi-run-hmms](../../programs/anvi-run-hmms)</span> <span class="artifact-r">[anvi-run-interacdome](../../programs/anvi-run-interacdome)</span> <span class="artifact-r">[anvi-run-kegg-kofams](../../programs/anvi-run-kegg-kofams)</span> <span class="artifact-r">[anvi-run-ncbi-cogs](../../programs/anvi-run-ncbi-cogs)</span> <span class="artifact-r">[anvi-run-pfams](../../programs/anvi-run-pfams)</span> <span class="artifact-r">[anvi-run-scg-taxonomy](../../programs/anvi-run-scg-taxonomy)</span> <span class="artifact-r">[anvi-run-trna-taxonomy](../../programs/anvi-run-trna-taxonomy)</span> <span class="artifact-r">[anvi-scan-trnas](../../programs/anvi-scan-trnas)</span> <span class="artifact-r">[anvi-search-functions](../../programs/anvi-search-functions)</span> <span class="artifact-r">[anvi-search-palindromes](../../programs/anvi-search-palindromes)</span> <span class="artifact-r">[anvi-search-sequence-motifs](../../programs/anvi-search-sequence-motifs)</span> <span class="artifact-r">[anvi-show-misc-data](../../programs/anvi-show-misc-data)</span> <span class="artifact-r">[anvi-split](../../programs/anvi-split)</span> <span class="artifact-r">[anvi-summarize](../../programs/anvi-summarize)</span> <span class="artifact-r">[anvi-summarize-blitz](../../programs/anvi-summarize-blitz)</span> <span class="artifact-r">[anvi-update-db-description](../../programs/anvi-update-db-description)</span> <span class="artifact-r">[anvi-update-structure-database](../../programs/anvi-update-structure-database)</span> <span class="artifact-r">[anvi-script-add-default-collection](../../programs/anvi-script-add-default-collection)</span> <span class="artifact-r">[anvi-script-estimate-metabolic-independence](../../programs/anvi-script-estimate-metabolic-independence)</span> <span class="artifact-r">[anvi-script-filter-hmm-hits-table](../../programs/anvi-script-filter-hmm-hits-table)</span> <span class="artifact-r">[anvi-script-gen-distribution-of-genes-in-a-bin](../../programs/anvi-script-gen-distribution-of-genes-in-a-bin)</span> <span class="artifact-r">[anvi-script-gen-genomes-file](../../programs/anvi-script-gen-genomes-file)</span> <span class="artifact-r">[anvi-script-get-hmm-hits-per-gene-call](../../programs/anvi-script-get-hmm-hits-per-gene-call)</span> <span class="artifact-r">[anvi-script-merge-collections](../../programs/anvi-script-merge-collections)</span> <span class="artifact-r">[anvi-script-permute-trnaseq-seeds](../../programs/anvi-script-permute-trnaseq-seeds)</span></p>
+<p style="text-align: left" markdown="1"><span class="artifact-r">[anvi-cluster-contigs](../../programs/anvi-cluster-contigs)</span> <span class="artifact-r">[anvi-compute-completeness](../../programs/anvi-compute-completeness)</span> <span class="artifact-r">[anvi-db-info](../../programs/anvi-db-info)</span> <span class="artifact-r">[anvi-delete-functions](../../programs/anvi-delete-functions)</span> <span class="artifact-r">[anvi-delete-hmms](../../programs/anvi-delete-hmms)</span> <span class="artifact-r">[anvi-display-contigs-stats](../../programs/anvi-display-contigs-stats)</span> <span class="artifact-r">[anvi-display-metabolism](../../programs/anvi-display-metabolism)</span> <span class="artifact-r">[anvi-display-structure](../../programs/anvi-display-structure)</span> <span class="artifact-r">[anvi-draw-kegg-pathways](../../programs/anvi-draw-kegg-pathways)</span> <span class="artifact-r">[anvi-estimate-genome-completeness](../../programs/anvi-estimate-genome-completeness)</span> <span class="artifact-r">[anvi-estimate-metabolism](../../programs/anvi-estimate-metabolism)</span> <span class="artifact-r">[anvi-estimate-scg-taxonomy](../../programs/anvi-estimate-scg-taxonomy)</span> <span class="artifact-r">[anvi-estimate-trna-taxonomy](../../programs/anvi-estimate-trna-taxonomy)</span> <span class="artifact-r">[anvi-export-contigs](../../programs/anvi-export-contigs)</span> <span class="artifact-r">[anvi-export-functions](../../programs/anvi-export-functions)</span> <span class="artifact-r">[anvi-export-gene-calls](../../programs/anvi-export-gene-calls)</span> <span class="artifact-r">[anvi-export-gene-coverage-and-detection](../../programs/anvi-export-gene-coverage-and-detection)</span> <span class="artifact-r">[anvi-export-locus](../../programs/anvi-export-locus)</span> <span class="artifact-r">[anvi-export-misc-data](../../programs/anvi-export-misc-data)</span> <span class="artifact-r">[anvi-export-splits-and-coverages](../../programs/anvi-export-splits-and-coverages)</span> <span class="artifact-r">[anvi-export-splits-taxonomy](../../programs/anvi-export-splits-taxonomy)</span> <span class="artifact-r">[anvi-gen-fixation-index-matrix](../../programs/anvi-gen-fixation-index-matrix)</span> <span class="artifact-r">[anvi-gen-gene-consensus-sequences](../../programs/anvi-gen-gene-consensus-sequences)</span> <span class="artifact-r">[anvi-gen-gene-level-stats-databases](../../programs/anvi-gen-gene-level-stats-databases)</span> <span class="artifact-r">[anvi-gen-structure-database](../../programs/anvi-gen-structure-database)</span> <span class="artifact-r">[anvi-gen-variability-profile](../../programs/anvi-gen-variability-profile)</span> <span class="artifact-r">[anvi-get-aa-counts](../../programs/anvi-get-aa-counts)</span> <span class="artifact-r">[anvi-get-codon-frequencies](../../programs/anvi-get-codon-frequencies)</span> <span class="artifact-r">[anvi-get-codon-usage-bias](../../programs/anvi-get-codon-usage-bias)</span> <span class="artifact-r">[anvi-get-metabolic-model-file](../../programs/anvi-get-metabolic-model-file)</span> <span class="artifact-r">[anvi-get-pn-ps-ratio](../../programs/anvi-get-pn-ps-ratio)</span> <span class="artifact-r">[anvi-get-sequences-for-gene-calls](../../programs/anvi-get-sequences-for-gene-calls)</span> <span class="artifact-r">[anvi-get-sequences-for-hmm-hits](../../programs/anvi-get-sequences-for-hmm-hits)</span> <span class="artifact-r">[anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam)</span> <span class="artifact-r">[anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene)</span> <span class="artifact-r">[anvi-get-split-coverages](../../programs/anvi-get-split-coverages)</span> <span class="artifact-r">[anvi-import-collection](../../programs/anvi-import-collection)</span> <span class="artifact-r">[anvi-import-functions](../../programs/anvi-import-functions)</span> <span class="artifact-r">[anvi-import-misc-data](../../programs/anvi-import-misc-data)</span> <span class="artifact-r">[anvi-import-taxonomy-for-genes](../../programs/anvi-import-taxonomy-for-genes)</span> <span class="artifact-r">[anvi-inspect](../../programs/anvi-inspect)</span> <span class="artifact-r">[anvi-interactive](../../programs/anvi-interactive)</span> <span class="artifact-r">[anvi-merge](../../programs/anvi-merge)</span> <span class="artifact-r">[anvi-migrate](../../programs/anvi-migrate)</span> <span class="artifact-r">[anvi-profile-blitz](../../programs/anvi-profile-blitz)</span> <span class="artifact-r">[anvi-reaction-network](../../programs/anvi-reaction-network)</span> <span class="artifact-r">[anvi-refine](../../programs/anvi-refine)</span> <span class="artifact-r">[anvi-rename-bins](../../programs/anvi-rename-bins)</span> <span class="artifact-r">[anvi-run-cazymes](../../programs/anvi-run-cazymes)</span> <span class="artifact-r">[anvi-run-hmms](../../programs/anvi-run-hmms)</span> <span class="artifact-r">[anvi-run-interacdome](../../programs/anvi-run-interacdome)</span> <span class="artifact-r">[anvi-run-kegg-kofams](../../programs/anvi-run-kegg-kofams)</span> <span class="artifact-r">[anvi-run-ncbi-cogs](../../programs/anvi-run-ncbi-cogs)</span> <span class="artifact-r">[anvi-run-pfams](../../programs/anvi-run-pfams)</span> <span class="artifact-r">[anvi-run-scg-taxonomy](../../programs/anvi-run-scg-taxonomy)</span> <span class="artifact-r">[anvi-run-trna-taxonomy](../../programs/anvi-run-trna-taxonomy)</span> <span class="artifact-r">[anvi-scan-trnas](../../programs/anvi-scan-trnas)</span> <span class="artifact-r">[anvi-search-functions](../../programs/anvi-search-functions)</span> <span class="artifact-r">[anvi-search-palindromes](../../programs/anvi-search-palindromes)</span> <span class="artifact-r">[anvi-search-sequence-motifs](../../programs/anvi-search-sequence-motifs)</span> <span class="artifact-r">[anvi-show-misc-data](../../programs/anvi-show-misc-data)</span> <span class="artifact-r">[anvi-split](../../programs/anvi-split)</span> <span class="artifact-r">[anvi-summarize](../../programs/anvi-summarize)</span> <span class="artifact-r">[anvi-summarize-blitz](../../programs/anvi-summarize-blitz)</span> <span class="artifact-r">[anvi-update-db-description](../../programs/anvi-update-db-description)</span> <span class="artifact-r">[anvi-update-structure-database](../../programs/anvi-update-structure-database)</span> <span class="artifact-r">[anvi-script-add-default-collection](../../programs/anvi-script-add-default-collection)</span> <span class="artifact-r">[anvi-script-estimate-metabolic-independence](../../programs/anvi-script-estimate-metabolic-independence)</span> <span class="artifact-r">[anvi-script-filter-hmm-hits-table](../../programs/anvi-script-filter-hmm-hits-table)</span> <span class="artifact-r">[anvi-script-gen-distribution-of-genes-in-a-bin](../../programs/anvi-script-gen-distribution-of-genes-in-a-bin)</span> <span class="artifact-r">[anvi-script-gen-genomes-file](../../programs/anvi-script-gen-genomes-file)</span> <span class="artifact-r">[anvi-script-get-hmm-hits-per-gene-call](../../programs/anvi-script-get-hmm-hits-per-gene-call)</span> <span class="artifact-r">[anvi-script-merge-collections](../../programs/anvi-script-merge-collections)</span> <span class="artifact-r">[anvi-script-permute-trnaseq-seeds](../../programs/anvi-script-permute-trnaseq-seeds)</span></p>
 
 
 ## Description