From e63bd57da0351b2c341227c284306f29c732a5a1 Mon Sep 17 00:00:00 2001 From: Quarto GHA Workflow Runner Date: Mon, 22 Jul 2024 08:15:10 +0000 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- accessing-ancient-metagenomic-data.html | 2 +- acknowledgements.html | 2 +- ancient-metagenomic-pipelines.html | 12 +- appendices.html | 2 +- authentication.html | 116 +- authors.html | 2 +- bare-bones-bash.html | 2 +- before-you-start.html | 2 +- chapter-checklist.html | 4 +- chapter-template.html | 53 +- chapter-writing-guidelines.html | 113 +- citing-this-book.html | 2 +- contamination.html | 2 +- denovo-assembly.html | 12 +- deprecated-chapters.html | 2 +- foreword.html | 2 +- functional-profiling.html | 2 +- genome-mapping.html | 2 +- git-github.html | 2 +- index.html | 2 +- introduction-to-ancient-dna.html | 2 +- introduction-to-evolutionary-biology.html | 2 +- introduction-to-metagenomics.html | 2 +- introduction-to-microbial-genomics.html | 2 +- introduction-to-ngs-sequencing.html | 2 +- phylogenomics.html | 2 +- python-pandas.html | 1110 +++++++++--------- r-tidyverse.html | 2 +- resources.html | 2 +- search.json | 84 +- section-ancient-genomics.html | 2 +- section-ancient-metagenomic-resources.html | 2 +- section-ancient-metagenomics.html | 2 +- section-theory.html | 2 +- section-useful-skills.html | 2 +- sitemap.xml | 72 +- taxonomic-profiling.html | 1197 ++++++++++---------- tools.html | 2 +- 39 files changed, 1418 insertions(+), 1413 deletions(-) diff --git a/.nojekyll b/.nojekyll index 735a922f..af15625b 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -3581973d \ No newline at end of file +3c1cdbe4 \ No newline at end of file diff --git a/accessing-ancient-metagenomic-data.html b/accessing-ancient-metagenomic-data.html index b748f6ea..ee777c3f 100644 --- a/accessing-ancient-metagenomic-data.html +++ b/accessing-ancient-metagenomic-data.html @@ -302,7 +302,7 @@
  • - 11  Introduction to de novo Genome Assembly + 11  De novo Genome Assembly
  • diff --git a/acknowledgements.html b/acknowledgements.html index 0cb65c40..99f99b12 100644 --- a/acknowledgements.html +++ b/acknowledgements.html @@ -247,7 +247,7 @@
  • - 11  Introduction to de novo Genome Assembly + 11  De novo Genome Assembly
  • diff --git a/ancient-metagenomic-pipelines.html b/ancient-metagenomic-pipelines.html index f68b4da0..a53fc223 100644 --- a/ancient-metagenomic-pipelines.html +++ b/ancient-metagenomic-pipelines.html @@ -302,7 +302,7 @@
  • - 11  Introduction to de novo Genome Assembly + 11  De novo Genome Assembly
  • @@ -1288,9 +1288,8 @@ 

    conda activate aMeta
 cd /<path/<to>/ancient-metagenomic-pipelines/aMeta/

    Finally, we are ready to run aMeta, where it will automatically pick up our config and samplesheet file we placed in config/!

    -
    #| eval: false
-## change conda-frontend to mamba if we set this up earlier!
-snakemake --snakefile workflow/Snakefile --use-conda -j 10 --conda-frontend conda
    +
    ## change conda-frontend to mamba if we set this up earlier!
+snakemake --snakefile workflow/Snakefile --use-conda -j 10 --conda-frontend conda
    @@ -1454,7 +1453,7 @@

    Firstly we need a method of validating that contigs are from an ancient genome (in nf-core/mag, damage patterns are generated by pyDamage).

    Secondly, to correct for falsely included damage bases in contigs in some contexts. As previously stated a previous chapter by Alex Hübner:

    -

    In our group we realised that the gene sequences that were annotated on the contigs of MEGAHIT tended to have a higher number of nonsense mutations compared to the known variants of the genes. After manual inspection, we observed that many of these mutations appeared because MEGAHIT chose the damage-derived T allele over the C allele or the damage-derived A allele over a G allele (see Klapper2023-mv?).

    +

    In our group we realised that the gene sequences that were annotated on the contigs of MEGAHIT tended to have a higher number of nonsense mutations compared to the known variants of the genes. After manual inspection, we observed that many of these mutations appeared because MEGAHIT chose the damage-derived T allele over the C allele or the damage-derived A allele over a G allele (see Klapper et al. 2023, fig. S1).

    To overcome this issue, my colleagues Maxime Borry, James Fellows Yates and I developed a strategy to replace these damage-derived alleles in the contig sequences. This approach consists of aligning the short-read data against the contigs, performing genotyping along them, and finally replacing all alleles for which we have strong support for an allele that is different from the one selected by MEGAHIT.

    @@ -1836,6 +1835,9 @@

    Kim, Daehwan, Li Song, Florian P Breitwieser, and Steven L Salzberg. 2016. “Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.” Genome Research 26 (12): 1721–29. https://doi.org/10.1101/gr.210641.116.

    +
    +Klapper, Martin, Alexander Hübner, Anan Ibrahim, Ina Wasmuth, Maxime Borry, Veit G Haensch, Shuaibing Zhang, et al. 2023. “Natural Products from Reconstructed Bacterial Genomes of the Middle and Upper Paleolithic.” Science (New York, N.Y.), May, eadf5300. https://doi.org/10.1126/science.adf5300. +
    Krakau, Sabrina, Daniel Straub, Hadrien Gourlé, Gisela Gabernet, and Sven Nahnsen. 2022. “Nf-Core/Mag: A Best-Practice Pipeline for Metagenome Hybrid Assembly and Binning.” NAR Genomics and Bioinformatics 4 (1). https://doi.org/10.1093/nargab/lqac007.
    diff --git a/appendices.html b/appendices.html index a48850be..2ba7cb71 100644 --- a/appendices.html +++ b/appendices.html @@ -246,7 +246,7 @@
  • - 11  Introduction to de novo Genome Assembly + 11  De novo Genome Assembly
  • diff --git a/authentication.html b/authentication.html index f11648be..76ba48df 100644 --- a/authentication.html +++ b/authentication.html @@ -305,7 +305,7 @@
  • - 11  Introduction to de novo Genome Assembly + 11  De novo Genome Assembly
  • @@ -930,23 +930,23 @@

    -
    - @@ -2794,8 +2794,8 @@

    diff --git a/tools.html b/tools.html index bc137f18..f4f39f95 100644 --- a/tools.html +++ b/tools.html @@ -247,7 +247,7 @@
  • - 11  Introduction to de novo Genome Assembly + 11  De novo Genome Assembly