Build a core-genome phylogeny - Revision history

Tpillone at 10:54, 31 October 2018

2018-10-31T10:54:49Z

2018-10-31T10:51:19Z

2018-10-31T10:50:00Z

2018-10-31T10:49:00Z

2018-10-31T10:48:17Z

2018-10-31T10:47:44Z

2018-10-31T10:45:38Z

2018-10-31T10:44:10Z

2018-10-24T14:13:08Z

2018-10-24T13:51:43Z

@@ Line 165: / Line 165: @@
 <syntaxhighlight lang="Bash" line='line'>
 for i in `ls *gbff`; do
      gbk2faa.py -i $i -f
 done
@@ Line 180: / Line 182: @@
 <syntaxhighlight lang="Bash" line='line'>
+# -t number of threads
 </syntaxhighlight>
 === Results ===
-Orthofinder will take a while because it needs to BLAST all pairs of genomes. Once terminated, the phylogeny can be found in:
+Orthofinder will take a while because it needs to BLAST all pairs of genomes (>24h in my single test with 6 threads). Once terminated, the phylogeny can be found in:
 <syntaxhighlight lang="Bash" line='line'>

@@ Line 161: / Line 161: @@
 </syntaxhighlight>
-Now we need to extract predicted protein sequenced for each genome
+Now we need to extract predicted protein sequences from the gbff file for each genome
 <syntaxhighlight lang="Bash" line='line'>

@@ Line 135: / Line 135: @@
 === Download gbff files ===
-* The 106 assemblies can be downloaded based on their refseq accessions (e.g GCA_000424105.1).
+* The 106 (+ eventually 3 Robinsoniella) assemblies can be downloaded based on their refseq accessions (e.g GCA_000424105.1).
 * With the option -g, only the gbff file will be downloaded (sequence + annotations in [https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html genbank format])

@@ Line 131: / Line 131: @@
 </syntaxhighlight>
-* there is curently 4 assemblies abailable for this genus. You can add them to the initial table.
+* there is curently 4 assemblies available for this genus. You can add them to the initial table if not already present.
 === Download gbff files ===

@@ Line 126: / Line 126: @@
 # -t taxid
 # -rs only refseq assemblies
-# -d get a table with all assemblies available
+# -d get all assemblies available
 # -o output file
 get_ncbi_genome_assemblies.py -t 588605 -rs -d -o robinsoniella_assemblies.tab

@@ Line 121: / Line 121: @@
 * the table can be manually edited to add/remove assemblies
-* For instance, if you are particular interested in one particular genus (eg. Robinsoniella genus, NCBI taxid 588605), you can add all available assemblies for this specific genus. For this you need to use the "-d" parameter (Report complete list of assemblies).
+* For instance, if you are interested in one particular genus (eg. Robinsoniella genus, NCBI taxid 588605), you can add all available assemblies for this specific genus. For this you need to use the "-d" parameter (Report complete list of assemblies).
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← Older revision		Revision as of 14:13, 24 October 2018
Line 173:		Line 173:

	</syntaxhighlight>		</syntaxhighlight>
		+
		+	=== Results ===
		+
		+	Orthofinder will take a while because it needs to BLAST all pairs of genomes. Once terminated, the phylogeny can be found in:
		+
		+	<syntaxhighlight lang="Bash" line='line'>
		+	cd faa/Results_Oct/WorkingDirectory/Orthologues_/SpeciesTree_rooted.txt
		+	</syntaxhighlight>
		+
		+	The tree can be visualized with [http://tree.bio.ed.ac.uk/software/figtree/ figtree]. Leaf labels will be the faa file names. They can be renamed using gbk files with the follwing script:
		+
		+	<syntaxhighlight lang="Bash" line='line'>
		+	phylo_convert_leaf_labels.py -i SpeciesTree_rooted.txt -g <path/to/gbff/files/*gbff>
		+	</syntaxhighlight>
		+
		+	The resulting tree will be named "SpeciesTree_rooted_renamed.txt".

@@ Line 147: / Line 147: @@
 <syntaxhighlight lang="Bash" line='line'>
 mkdir gbk_files
-mv ../GC*/*gz gbk_files
+mv GC*/*gz gbk_files
 cd gbk_files
 gunzip *gz
@@ Line 163: / Line 163: @@
 <syntaxhighlight lang="Bash" line='line'>
-mkdir -f orthofinder/faa
+mkdir -fp orthofinder/faa
 mv *faa orthofinder/faa
 cd orthofinder
@@ Line 171: / Line 171: @@
 <syntaxhighlight lang="Bash" line='line'>
-mkdir -f orthofinder/faa
 </syntaxhighlight>