From 6db2341b84bb691dea43ab99e573051331d13bdc Mon Sep 17 00:00:00 2001 From: misialq Date: Wed, 6 Nov 2024 08:54:12 +0000 Subject: [PATCH] deploy: d2035990a86e6b727f96bd7fd6c707750f75afa0 --- _sources/chapters/01_filtering/host-filtering.md | 4 ++++ _sources/chapters/02_mag_reconstruction/reconstruction.md | 2 +- chapters/01_filtering/host-filtering.html | 3 +++ chapters/02_mag_reconstruction/reconstruction.html | 2 +- searchindex.js | 2 +- 5 files changed, 10 insertions(+), 3 deletions(-) diff --git a/_sources/chapters/01_filtering/host-filtering.md b/_sources/chapters/01_filtering/host-filtering.md index 8502b4a..53c88e0 100644 --- a/_sources/chapters/01_filtering/host-filtering.md +++ b/_sources/chapters/01_filtering/host-filtering.md @@ -12,6 +12,10 @@ kernelspec: name: python3 --- # Host read removal +There are a few different options to perform host read removal in QIIME 2: a more generic one using the `filter-reads` action +and a more specific one using the `filter-reads-pangenome` action. Below you can see how to use both of them. In this tutorial we will +use the `filter-reads-pangenome` action to remove human reads from the dataset. + ## Removal of contaminating reads Removal of contaminating reads can generally be done by mapping the reads to a reference database and filtering out the reads that map to it. In QIIME 2 this can be done by using the `filter-reads` action from the `quality-control` plugin. Before the filtering diff --git a/_sources/chapters/02_mag_reconstruction/reconstruction.md b/_sources/chapters/02_mag_reconstruction/reconstruction.md index 3fa69ab..abaa0fc 100644 --- a/_sources/chapters/02_mag_reconstruction/reconstruction.md +++ b/_sources/chapters/02_mag_reconstruction/reconstruction.md @@ -34,7 +34,7 @@ genetic information for the next steps of our analysis. ``` ```{code-cell} qiime assembly assemble-megahit \ - --i-seqs ./cache:reads_paired \ + --i-seqs ./cache:reads_filtered \ --p-presets "meta-sensitive" \ --p-num-cpu-threads 24 \ --p-min-contig-len 200 \ diff --git a/chapters/01_filtering/host-filtering.html b/chapters/01_filtering/host-filtering.html index 8fa9b7c..14fc46b 100644 --- a/chapters/01_filtering/host-filtering.html +++ b/chapters/01_filtering/host-filtering.html @@ -339,6 +339,9 @@

Contents

Host read removal#

+

There are a few different options to perform host read removal in QIIME 2: a more generic one using the filter-reads action +and a more specific one using the filter-reads-pangenome action. Below you can see how to use both of them. In this tutorial we will +use the filter-reads-pangenome action to remove human reads from the dataset.

Removal of contaminating reads#

Removal of contaminating reads can generally be done by mapping the reads to a reference database and filtering out the reads diff --git a/chapters/02_mag_reconstruction/reconstruction.html b/chapters/02_mag_reconstruction/reconstruction.html index 366c549..6eb16b1 100644 --- a/chapters/02_mag_reconstruction/reconstruction.html +++ b/chapters/02_mag_reconstruction/reconstruction.html @@ -370,7 +370,7 @@

Assemble contigs with MEGAHIT 
qiime assembly assemble-megahit \
-    --i-seqs ./cache:reads_paired \
+    --i-seqs ./cache:reads_filtered \
     --p-presets "meta-sensitive" \          
     --p-num-cpu-threads 24 \                      
     --p-min-contig-len 200 \ 
diff --git a/searchindex.js b/searchindex.js
index 6fcd41e..e18ae49 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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