millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-13 07:13:10 +00:00
Code Issues Releases Packages Activity

[skip ci]

Browse source 
Add description for MALT
This commit is contained in:
Sofia Stamouli 2022-10-12 12:56:54 +02:00 committed by GitHub
parent 0b16010b92
commit e98cd038c7
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 17 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

18
docs/usage.md
View file

@ -440,8 +440,24 @@ Kraken2 allows the user to build custom databases. You can follow Kraken2 [tutor
Centrifuge is similar to Kraken2 in that it enables to [build custom databases](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database).
#### Kaiju
WIP
It is possible to [create custom databases](https://github.com/bioinformatics-centre/kaiju#custom-database) with Kaiju.
#### 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)
```bash
wget https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Feb2022.db.zip
unzip megan-nucl-Feb2022.db
malt-build -i path/to/fasta/files/*.{fna,fa} -s DNA -d index -t 8 -st 4 -a2t megan-nucl-Feb2022.db
```
#### Bracken
#### KrakenUniq
#### DIAMOND
#### mOTUs
## Troubleshooting and FAQs