pogenom linked

README.md

@@ -36,7 +36,7 @@ We use [PhyloPhlAn](https://huttenhower.sph.harvard.edu/phylophlan) to find the
 To find which strains are common to several samples based on reads and potentially linked to reconstructed genomes, we use [StrainPhlAn](http://segatalab.cibio.unitn.it/tools/strainphlan/).
 
 ### Part 8: [Analysis of intra- and inter-population variability](pogenom.md)
-In this step, single nucleotide variants (SNVs) are used to examine the intra- and inter-population variability of the population-level genomes which were in common between different samples using Pogenom.
+In this step, single nucleotide variants (SNVs) are used to examine the intra- and inter-population variability of the population-level genomes which were in common between different samples using [Pogenom](https://github.com/EnvGen/POGENOM).
 * [Coverage_Bins.R](Coverage_Bins.R)
 * [getSize](getSize)
 * [Breadth.R](Breadth.R)

pogenom.md

@@ -86,7 +86,7 @@ samtools index downsampled. ${BinName}.RG.merged.bam downsampled. ${BinName}.RG.
 freebayes -f cluster.${BinName}.fa -C 4 -p 1 --pooled-continuous --read-max-mismatch-fraction 0.05 --min-alternate-fraction 0.01 downsampled.${BinName}.RG.merged.bam | vcffilter -f "QUAL > 15" > downsampled.${BinName}.MERGED.index.vcf
 ```
 
-The resulting .vcf file for each group of bins is then used as input to [Pogenom](http://envgen.github.io/), which calculates the intra- and interpopulation diversities, amongst other useful data. Pogenom also takes as input the number of bins in the group, which can be found in the .vcf file (`$num`).
+The resulting .vcf file for each group of bins is then used as input to [Pogenom](https://github.com/EnvGen/POGENOM), which calculates the intra- and interpopulation diversities, amongst other useful data. Pogenom also takes as input the number of bins in the group, which can be found in the .vcf file (`$num`).
 
 ```
 num=$((`grep "#CHROM" downsampled.${BinName}.MERGED.index.vcf  | wc -w` - 9))