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Add tutorials section

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Sofia Stamouli 2022-10-12 11:39:03 +02:00 committed by GitHub
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@ -228,7 +228,7 @@ Activating this functionality will concatenate the FASTQ files with the same sam
You can optionally save the FASTQ output of the run merging with the `--save_runmerged_reads`. You can optionally save the FASTQ output of the run merging with the `--save_runmerged_reads`.
##### Profiling #### Profiling
###### MALT ###### MALT
@ -429,6 +429,20 @@ We recommend adding the following line to your environment to limit this (typica
NXF_OPTS='-Xms1g -Xmx4g' NXF_OPTS='-Xms1g -Xmx4g'
``` ```
## Tutorials
### Tutorial - How to create your custom database
#### 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).
#### Centrifuge
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
## Troubleshooting and FAQs ## Troubleshooting and FAQs
### I get a warning during centrifuge_kreport process with exit status 255. ### I get a warning during centrifuge_kreport process with exit status 255.