From ad7b642b89e09d73374371ed86f912fcc4b5d6d2 Mon Sep 17 00:00:00 2001
From: Anna Buschart <anna.buschart@uni.lu>
Date: Mon, 12 Jun 2017 09:52:49 +0200
Subject: [PATCH] pogenom linked
---
README.md | 2 +-
pogenom.md | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index f283bf8..733c79e 100644
--- a/README.md
+++ b/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)
diff --git a/pogenom.md b/pogenom.md
index 12062e2..7304b53 100644
--- a/pogenom.md
+++ b/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))
--
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