S

    Glossary

    Taxonomic profile

    A tab-separated table containing the estimated abundances of GTDB taxons in a metagenome. It is in TSV format with 3 columns, with each row corresponding to a taxon. A taxonomic profile may also be called a condensed profile, since it is the output of the condense algorithm within the main pipe workflow. Taxonomic profiles can be converted to other formats using singlem summarise. Columns:

    1. sample name. A taxonomic profile can consist of more than one sample. Usually all the taxons in the first sample are listed, and then the taxons in the second sample, and so on.
    2. coverage of that taxon. This is an approximation of the total read coverage of all genomes from this taxon. However, note that this coverage does not include the coverage of sub-taxons (It is [unfilled](/Glossary#Coverage, unfilled coverage and filled coverage)). For instance, the coverage of a species is not included in the coverage shown for its genus.
    3. taxonomy string of the taxon
    sample      coverage  taxonomy
ERR1914274  0         Root
ERR1914274  3.16      Root; d__Bacteria
ERR1914274  0         Root; d__Bacteria; p__Pseudomonadota
ERR1914274  0.06      Root; d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria
ERR1914274  0         Root; d__Bacteria; p__Bacillota_A
ERR1914274  0.61      Root; d__Bacteria; p__Bacillota_A; c__Clostridia
ERR1914274  0         Root; d__Bacteria; p__Bacteroidota
ERR1914274  0.39      Root; d__Bacteria; p__Bacteroidota; c__Bacteroidia
ERR1914274  0         Root; d__Bacteria; p__Bacillota
...

    OTU table

    A table containing window sequences per metagenome/contig and marker gene. It may be in default form (a TSV with 6 columns, like below), or an extended form with more detail in further columns. The default OTU table output from pipe, renew and summarise subcommands has 6 columns, with one sequence per row. The extended form OTU table and archive OTU tables have further information (see below). Columns of a default OTU table:

    1. marker name
    2. sample name
    3. sequence of the OTU
    4. number of reads detected from that OTU
    5. estimated coverage of a genome from this OTU
    6. A taxonomic classification for the OTU. This is a rough taxonomy which is refined during the "condense" step of the pipe workflow.
    gene                             sample        sequence            num_hits coverage  taxonomy
4.21.ribosomal_protein_S19_rpsS  my_sequences  TGGTCGCGCCGTT...    1        1.64      Root; d__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfuromonadales
4.21.ribosomal_protein_S19_rpsS  my_sequences  TGGTCGCGGCGCT...    1        1.64      Root; d__Bacteria; p__Acidobacteria; c__Solibacteres; o__Solibacterales; f__Solibacteraceae; g__Candidatus_Solibacter; s__Candidatus_Solibacter_usitatus

    OTU table (extended form)

    The extended OTU table form generated with the --output-extras option to the pipe, renew and summarise subcommands, has all the columns of a regular OTU table, but with several additional columns which contain more information about each OTU:

    1. read_names - the names of the reads which encode the OTU sequence
    2. nucleotides_aligned - the number of nucleotides which aligned to the window (usually 60, but can be more or less if there are gaps or inserts)
    3. taxonomy_by_known? - whether the taxonomy of the OTU was determined by known genomes (TRUE) or by the reads themselves (FALSE). Currently this is a disused column and is always marked FALSE.
    4. read_unaligned_sequences - the raw sequences of the reads which encode the OTU sequence
    5. equal_best_hit_taxonomies - the taxonomies of the best hits to the OTU sequence, if there are multiple equally good hits. This is a JSON array of strings.

    Archive OTU table

    Similar to an extended form OTU table, but in JSON form for machine readability and with formatting version recorded. The renew subcommand which re-analyses a dataset requires this format of OTU table rather than the default tab-separated OTU table format. The canonical file extension for SingleM packages is .json.

    Coverage, unfilled coverage and filled coverage

    First, to define coverage. Coverage of a single species is defined in the standard way as in e.g. CoverM. It is the average number of reads covering each position in that species' genome. SingleM (and Lyrebird) do not directly calculate this via mapping, but instead assume that the coverage of a species' single copy marker genes is representative of the coverage of the whole genome. In particular, it is estimated from the reads that encode sequences recruited to the highly conserved marker gene windows.

    In a standard taxonomic profile output by pipe, the coverage column is unfilled coverage. This means that the coverage of a taxon does not include the coverage of its sub-taxons. For example, in this profile:

    sample	    coverage  taxonomy
ERR1914274	0         Root
ERR1914274	3.1	      Root; d__Bacteria
ERR1914274	4.0	      Root; d__Bacteria; p__Pseudomonadota
ERR1914274	2.9	      Root; d__Archaea

    The unfilled coverage of d__Bacteria is 3.1. This means that SingleM estimates that 3.1x read coverage of bacterial genomes that do not belong to p__Pseudomonadota (the only sub-taxon of d__Bacteria listed).

    The filled coverage of d__Bacteria is 7.1, calculated as the coverage of d__Bacteria (3.1) plus the coverage of all of its descendents (Here just p__Pseudomonadota so 4.0).

    To calculate relative abundance, the filled coverage is used. For example, the relative abundance of d__Bacteria in the above profile is 7.1 / (7.1 + 2.9) = 0.71 or 71%. The relative abundance of p__Pseudomonadota is 4.0 / (7.1 + 2.9) = 0.40 or 40%.

    The coverage of a genus is the sum of the coverages of all its species, and so on up the taxonomic tree.

    SingleM package (spkg)

    Reference data for one particular marker gene and its window position. The canonical file extension for SingleM packages is .spkg.

    SingleM metapackage (smpkg)

    A collection of SingleM packages, with additional indices. The canonical file extension for SingleM metapackages is .smpkg.

    SingleM database

    An OTU table which has been converted to SQLite3 format and sequence similarity search indexes. Canonically SingleM databases are named with the .sdb extension, but this is not enforced. SingleM databases are created with the makedb subcommand, and queried with the query subcommand.

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