Merge branch 'main' of github.com:SPAAM-community/intro-to-ancient-metagenomics-book

Author: jfy133

authentication.qmd

@@ -475,7 +475,7 @@ For custom reference genomes not covered by NCBI, their accession IDs and the co
 The `ngsLCA` program considers a chosen similarity interval between each read and its reference in the generated bam/sam file.
 The similarity can be set as an edit distance `[-editdist[min/max]]`, i.e., number of mismatches between the read to reference genome, or as a similarity distance `[-simscore[low/high]]`, i.e., percentage of mismatches between the read to reference genome. 
 
-The main files produced by this command have the extensions `.bdamage.gz`, `lca.gz` and 'stat.gz'.
+The main files produced by this command have the extensions `.bdamage.gz`, `lca.gz` and `stat.gz`.
 The first consists of a nucleotide misincorporation matrix (also called **mismatch matrix**) which represents the nucleotide substitution counts across the reads (@tbl-authentication-examplecodetable2).
 The lca file reports the sequences analysed and their taxonomic paths, while the stat file includes other statistics (gc content, fragment length).
 
@@ -582,7 +582,7 @@ We also need the taxonomy files, which are in the folder `metadmg/small_taxonomy
 The best documentation is currently found in the –help function.
 :::
 
-metaDMG is installed in the conda environment 'authentication`. If not activated yet, we run 
+metaDMG is installed in the conda environment `authentication`. If not activated yet, we run 
 
 ```bash
 conda activate authentication