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Sofia Stamouli 2023-01-17 15:50:10 +01:00
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docs/output.md
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@ -261,7 +261,6 @@ The main taxonomic profiling file from KrakenUniq is the `*report.txt` file. Thi
You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `--krakenuniq_save_reads` and/or `--krakenuniq_save_readclassification` parameters to the pipeline.
### Centrifuge
[Centrifuge](https://github.com/DaehwanKimLab/centrifuge) is a taxonomic sequence classifier that uses a Burrows-Wheeler transform and Ferragina-Manzina index for storing and mapping sequences.
@ -322,7 +321,6 @@ The main output of MALT is the `.rma6` file format, which can be only loaded int
You will only recieve the `.sam` and `.megan` files if you supply `--malt_save_reads` and/or `--malt_generate_megansummary` parameters to the pipeline.
### MetaPhlAn3
[MetaPhlAn3](https://github.com/biobakery/metaphlan) is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level resolution via marker genes.
@ -340,6 +338,7 @@ You will only recieve the `.sam` and `.megan` files if you supply `--malt_save_r
</details>
The main taxonomic profiling file from MetaPhlAn3 is the `*_profile.txt` file. This provides the abundance estimates from MetaPhlAn3 however does not include raw counts by default.
### mOTUs
[mOTUS](https://github.com/motu-tool/mOTUs) maps reads to a unique marker specific database and estimates the relative abundance of known and unknown species.

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docs/usage.md
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@ -631,7 +631,6 @@ krakenuniq-build --db <DB_DIR_NAME> --kmer-len 31
Please see the [KrakenUniq documentation](https://github.com/fbreitwieser/krakenuniq#database-building) for more information.
#### MALT custom database
MALT does not provide any default databases for profiling, therefore you must build your own.
@ -640,7 +639,7 @@ In addition to the input directory, output directory, and the mapping file datab
```bash
malt-build -i <path>/<to>/<fasta>/*.{fna,fa,fasta} -a2t <path>/<to>/<map>.db -d <YOUR_DB_NAME>/ -s DNA
````
```
You can then add the <YOUR_DB_NAME>/ path to your nf-core/taxprofiler database input sheet.