mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:13:08 +00:00
Apply prettier
This commit is contained in:
parent
a622dcaef0
commit
98f3ab9fd1
1 changed files with 8 additions and 0 deletions
|
@ -484,15 +484,19 @@ NXF_OPTS='-Xms1g -Xmx4g'
|
||||||
### Tutorial - How to create your custom database
|
### Tutorial - How to create your custom database
|
||||||
|
|
||||||
#### Kraken2
|
#### Kraken2
|
||||||
|
|
||||||
Kraken2 allows the user to build custom databases. You can follow Kraken2 [tutorial](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases).
|
Kraken2 allows the user to build custom databases. You can follow Kraken2 [tutorial](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases).
|
||||||
|
|
||||||
#### Centrifuge
|
#### Centrifuge
|
||||||
|
|
||||||
Centrifuge allows the user to [build custom databases](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database).
|
Centrifuge allows the user to [build custom databases](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database).
|
||||||
|
|
||||||
#### Kaiju
|
#### Kaiju
|
||||||
|
|
||||||
It is possible to [create custom databases](https://github.com/bioinformatics-centre/kaiju#custom-database) with Kaiju.
|
It is possible to [create custom databases](https://github.com/bioinformatics-centre/kaiju#custom-database) with Kaiju.
|
||||||
|
|
||||||
#### MALT
|
#### MALT
|
||||||
|
|
||||||
To create a custom database for MALT, the user should download and unzip the following database which lists all NCBI records. The input files are specified using -i and the index is specified using -d. A detailed description for each argument can be found [here](https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf)
|
To create a custom database for MALT, the user should download and unzip the following database which lists all NCBI records. The input files are specified using -i and the index is specified using -d. A detailed description for each argument can be found [here](https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf)
|
||||||
|
|
||||||
```bash
|
```bash
|
||||||
|
@ -502,12 +506,15 @@ malt-build -i path/to/fasta/files/*.{fna,fa} -s DNA -d index -t 8 -st 4 -a2t meg
|
||||||
```
|
```
|
||||||
|
|
||||||
#### Bracken
|
#### Bracken
|
||||||
|
|
||||||
You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.shtml?t=manual) to build a custom database. Alternatively, you can use one of the indexes that can be found [here](https://benlangmead.github.io/aws-indexes/k2).
|
You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.shtml?t=manual) to build a custom database. Alternatively, you can use one of the indexes that can be found [here](https://benlangmead.github.io/aws-indexes/k2).
|
||||||
|
|
||||||
#### KrakenUniq
|
#### KrakenUniq
|
||||||
|
|
||||||
For KrakenUniq, we recommend using one of the available databases [here](https://benlangmead.github.io/aws-indexes/k2)
|
For KrakenUniq, we recommend using one of the available databases [here](https://benlangmead.github.io/aws-indexes/k2)
|
||||||
|
|
||||||
#### DIAMOND
|
#### DIAMOND
|
||||||
|
|
||||||
To create a custom database for DIAMOND, the user should download and unzip the NCBI's taxonomy files. The `makedb` needs to be executed afterwards. A detailed description can be found [here](https://gensoft.pasteur.fr/docs/diamond/0.8.22/diamond_manual.pdf)
|
To create a custom database for DIAMOND, the user should download and unzip the NCBI's taxonomy files. The `makedb` needs to be executed afterwards. A detailed description can be found [here](https://gensoft.pasteur.fr/docs/diamond/0.8.22/diamond_manual.pdf)
|
||||||
|
|
||||||
```bash
|
```bash
|
||||||
|
@ -524,6 +531,7 @@ rm *dmp *txt *gz *prt *zip
|
||||||
```
|
```
|
||||||
|
|
||||||
#### mOTUs
|
#### mOTUs
|
||||||
|
|
||||||
A detailed description on how to download mOTUs database can be found [here](https://github.com/motu-tool/mOTUs)
|
A detailed description on how to download mOTUs database can be found [here](https://github.com/motu-tool/mOTUs)
|
||||||
|
|
||||||
## Troubleshooting and FAQs
|
## Troubleshooting and FAQs
|
||||||
|
|
Loading…
Reference in a new issue