From df8d24c78f9b4dab33b7886a807123de63ca7342 Mon Sep 17 00:00:00 2001 From: Oskar Karlsson Date: Wed, 22 Feb 2017 21:05:13 +0100 Subject: [PATCH 1/2] Update wms.md --- wms.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/wms.md b/wms.md index 148349e..9f6e19d 100644 --- a/wms.md +++ b/wms.md @@ -1,5 +1,7 @@ # Whole Metagenome Sequencing +In this tutorial you'll analyze a samples from human and pig put metagenomes. + ### Table of Contents * [Introduction](#introduction) @@ -28,13 +30,14 @@ The Human Microbiome: Whole Metagenome sequencing (WMS), or shotgun metagenome sequencing, is a relatively new and powerful sequencing approach that provides insight into community biodiversity and function. On the contrary of Metabarcoding, where only a specific region of the bacterial community (the 16s rRNA) is sequenced, WMS aims at sequencing all the genomic material present in the environment. -The choice of shotgun or 16S approaches is usually dictated by the nature of the studies being conducted. For instance, 16S is well suited for analysis of large number of samples, i.e., multiple patients, longitudinal studies, etc. but offers limited taxonomical and functional resolution. WMS is generally more expensive but offers increased resolution, and allows the discovery of archaea and viruses. +The choice of shotgun or 16S approaches is usually dictated by the nature of the studies being conducted. For instance, 16S is well suited for analysis of large number of samples, i.e., multiple patients, longitudinal studies, etc. but offers limited taxonomical and functional resolution. WMS is generally more expensive but offers increased resolution, and allows the discovery of viruses as well as other mobile genetic elements. ### Softwares Required for this Tutorial * [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) * [Kraken](https://ccb.jhu.edu/software/kraken/) -* [Bracken](https://github.com/jenniferlu717/Bracken) +* [Bracken](http://ccb.jhu.edu/software/bracken/) +* [R](https://www.r-project.org/) * [Pavian](https://github.com/fbreitwieser/pavian) ### Getting the Data and Checking their Quality From 0a590d35d7a513b2186af8814de5b10ee7951381 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hadrien=20Gourl=C3=A9?= Date: Wed, 22 Feb 2017 21:10:35 +0100 Subject: [PATCH 2/2] Update wms.md removed first sentence --- wms.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/wms.md b/wms.md index 9f6e19d..98c8d99 100644 --- a/wms.md +++ b/wms.md @@ -1,7 +1,5 @@ # Whole Metagenome Sequencing -In this tutorial you'll analyze a samples from human and pig put metagenomes. - ### Table of Contents * [Introduction](#introduction)