diff --git a/materials/22-pract.md b/materials/22-pract.md index ac5886f..84130a8 100644 --- a/materials/22-pract.md +++ b/materials/22-pract.md @@ -76,7 +76,7 @@ mixedcomm_reverse_unpaired.fq.gz ## Compositional mapping of shotgun metagenomics data -The previously used whole-genome alignment based mapping method works very well if we know what we are looking for, e.g., we try to detect a known pathogen or follow the dynamic changes in a synthetic community. When we try to describe the composition of more complex communities the potential reference database would be so big using whole genomes (Bacteria + Archea + Fungi + Virus), so we apply different reduction strategies. The two main approaches are:(i) Finding biologically meaningful genetic signatures (e.g., genes that are only present in certain taxonomic group) and search for those in the raw data; (ii) extract numerous random short fragments from genomes and try to find exact matchings for those in the raw data. +When we try to describe the composition of more complex communities the potential reference database would be so big using whole genomes (Bacteria + Archea + Fungi + Virus), so we apply different reduction strategies. The two main approaches are:(i) Finding biologically meaningful genetic signatures (e.g., genes that are only present in certain taxonomic group) and search for those in the raw data; (ii) extract numerous random short fragments from genomes and try to find exact matchings for those in the raw data. ### MASH, a random k-mer based profiling method @@ -158,7 +158,7 @@ Notice, that in both cases not only the query genome came up with high number of ```bash mash screen -w mixed_community.msh NZ_CP034931.fa -mash screen mixed_community.msh NZ_CP038419_1.fasta +mash screen mixed_community.msh NZ_CP034931.fa mash screen -w mixed_community.msh NZ_CP038419_1.fasta mash screen mixed_community_hr.msh NZ_CP038419_1.fasta