millironx/taxprofiler
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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. 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
[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. [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. 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
[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. [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> </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. 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
[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. [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. Please see the [KrakenUniq documentation](https://github.com/fbreitwieser/krakenuniq#database-building) for more information.
#### MALT custom database #### MALT custom database
MALT does not provide any default databases for profiling, therefore you must build your own. 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 ```bash
malt-build -i <path>/<to>/<fasta>/*.{fna,fa,fasta} -a2t <path>/<to>/<map>.db -d <YOUR_DB_NAME>/ -s DNA 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. You can then add the <YOUR_DB_NAME>/ path to your nf-core/taxprofiler database input sheet.