Taxonomic profiling using mOTUs with ngless¶

You can use ngless to compute mOTU profiles.

This requires the use of the (standard) motus module:

ngless "0.8"
import "motus" version "0.1"

This module (with the motus database) will be downloaded the first time you use it.

You can use all the ngless functionality to load and preprocess your data:

input = paired('input.1.fq.gz', 'input.2.fq.gz')

files = preprocess(input, keep_singles=False) using |read|:
    read = substrim(read, min_quality=25)
    if len(read) < 45:
        discard

Producing the motus tables is done in three steps.

Map the samples against the motus reference (this reference comes with the motus module we imported earlier):
```
mapped = map(files, reference='motus', mode_all=True)
```
call the built-in count function to summarize your reads at gene level, optionally adding include_minus1=true if you want to also obtain the fraction of unknown reads (-1). This is the default behavior from version 0.6 onwards:
```
counted = count(mapped, features=['gene'], multiple={dist1})
```
call the motus function, which takes the gene count table and performs the motus quantification. The result of this call is another table, which can then be written out with the standard write call:
```
table = motus(counted)
write(table, ofile='motus-counts.txt')
```

This function is the only special function introduced by the motus module, everything else is standard ngless.

You can see a full worked out example in the examples/motus.ngl recipe