standardise

What

The purpose of the standardise (aka standardize) command is to take the output of a single sample from a single taxonomic profiler and convert it into a standard format that is compatible with the output of other profilers standardised by taxpasta.

When

You should use taxpasta standardise when you want to standardise a single taxonomic profile or multiple profiles independently but do not want to merge them in a single table, for example, you wish to store them separately to merge them yourself in the future.

See merge if you wish to both standardise and merge in one step to generate a single table containing all samples.

Warning

You should only use this command if you are interested in raw 'counts'! The standardised output will remove profiler specific information, such as names, percentages, and lineage information.

How

To use this command, you need a single output file from a single taxonomic profiler, the name of the tool, and to specify an output file name:

taxpasta standardise --profiler kraken2 --output sample_standardised.tsv sample.kreport.txt

where sample.kreport.txt is a taxonomic profiling report file from kraken2.

This will produce a file called sample_standardised.tsv that contains the taxpasta 'standard' two column structure described below.

Tip

taxpasta standardise will automagically attempt to guess the output format based on the output file extension. You can alternatively explicitly define this with the --output-format flag. See taxpasta standardise --help for all supported formats.

Why

Take, for example, the following Kraken2 output file.

 99.98  787758  787758  U   0   unclassified
  0.02  119 0   R   1   root
  0.02  119 0   R1  131567    cellular organisms
  0.02  119 0   D   2759        Eukaryota
  0.02  119 0   D1  33154         Opisthokonta
  0.01  96  0   K   4751            Fungi
  0.01  96  0   K1  451864            Dikarya

This output format is specific to Kraken2 and is unlikely to be comparable with other tools, as they will record this information in different formats. Furthermore, the indentation system to show taxonomic rank depth is not particularly 'machine-readable'; making it difficult to load it into spreadsheet tools or tabular formats preferred by languages such as R.

A more common format in metagenomics is to have a first column with the taxon name and a second column with the number of sequence 'hits' against that particular taxon. Note that this format also encodes common information across most tools, whereas Kraken2 includes additional information that may not be reported by other profilers, such as a column with the fraction against a taxon of all hits.

We have chosen to reduce all taxa to their respective identifiers and a count. We chose zero as the identifier for unclassified reads. Since there are many downstream processing and analytics methods that assume integer read counts, we only support such a count or pseudo count column.

taxonomy_id	count
0	787758
1	119
131567	119
2759	119
33154	119
4751	96
451864	96

Taxpasta supports fairly diverse output formats but at the very least there should be a header indicating each column, the first (taxonomy_id) denoting which taxonomy identifier has the counts in the second column (count).

Info

This subcommand is used internally in the merge command prior to merging multiple profiles into one table.

Danger

Taxpasta will assume that all taxonomic profiles to be processed are based on the same underlying taxonomy. That means, taxpasta will happily join taxa by their identifier even if they stem from different taxonomies.