added pan_genome to index

Author: HadrienG

README.md

@@ -8,9 +8,10 @@ bioinformatics subjects:
 * [Introduction to Unix](unix/first_steps.md)
 * [File formats](file_formats.md)
 * [Quality Control](qc.md)
-* [Variant Calling](variant_calling.md)
 * [Assembly](assembly.md)
 * [Annotation](annotation.md)
+* [Variant Calling](variant_calling.md)
+* [Pan-genome Analysis](pan-genome.md)
 * [RNA-Seq](rna_seq.md)
 * [16s Metabarcoding Analysis](16s.md)
 * [Whole Metagenome Sequencing](wms.md)

pan_genome.md

@@ -9,7 +9,7 @@ This tutorial is inspired from [Genome annotation and Pangenome Analysis](https:
 We'll use six *Listeria monocytogenes* genomes in this tutorial.
 
 ```bash
-wget pangenome.tar.gz
+wget https://github.com/HadrienG/tutorials/blob/master/data/pangenome.tar.gz
 tar xzf pangenome.tar.gz
 cd pangenome
 ```
@@ -18,7 +18,7 @@ These genomes correspond to isolates of *L. monocytogenes* reported in
 
 > Xiangyu Deng, Adam M Phillippy, Zengxin Li, Steven L Salzberg and Wei Zhang. (2010) Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. doi:10.1186/1471-2164-11-500
 
-The six genomes you downaloaded were selected based on their level of completeness (finished; contigs, etc) and their genotype (type I-III):
+The six genomes you downloaded were selected based on their level of completeness (finished; contigs, etc) and their genotype (type I-III):
 
 Genome Assembly	| Genome Accession | Genotype | Sequenced by | Status
 --- | --- | --- | --- | ---
@@ -56,11 +56,11 @@ Roary comes with a python script that allows you to generate a few plots to grap
 First, we need to generate a tree file from the alignment generated by Roary:
 
 ```
-raxmlHPC -m GTRGAMMA -p 12345 -s core_gene_alignment.aln -n core.tre
+FastTree –nt –gtr core_gene_alignment.aln > my_tree.newick
 ```
 
 Then we can plot the Roary results:
 
 ```
-roary_plots.py RAxML_bestTree.core.tre gene_presence_absence.csv
+roary_plots.py my_tree.newick gene_presence_absence.csv
 ```