---
title: "Pipeline preparation: nf-core/createtaxdb"
tags: pipeline,createtaxdb,planning
---

## Required auxiliary files:

### Per Tool

Bracken
- read length

Centrifuge
- seq2taxid.map (sequence IDs to tax IDs
- taxonomy tree (node dump?)
- taxonomy ID to name

DIAMOND
- taxdump.zip (nodes.dump, names.dump?)
- prot.accession2taxid (just protein seq2taxid?)

Kaiju
- taxdump.zip (nodes and names dmp?)

Kraken2
- (taxdump) nodes and names dmp
- accession2taxid (seq2taxid?)

KrakenUniq
- seq2taxid.map
- taxonomy files (using KU DL?)

MALT
- Megandb

ganon
- taxonomy files (normally downloaded for you by ganon-build)

### Per file (common)

- taxdump.zip: diamond, kaiju, kraken2, krakenuniq, ganon
- nodes.dmp
- names.dmp
- seq2taxid (or possibly similar) karken2(?), diamond(>), centrifuge

## Modules

- [ ] bracken-build
- [ ] centrifuge-download
- [x] centrifuge-build
- [x] diamond-makedb
- [x] kaiju-mkbwt
- [x] kaiju-mkfmi
- [ ] kraken2-build (download taxonomy, add-to-library, build, clean)
- [x] krakenuniq_download
- [x] krakenuniq_build
- [x] malt-build
- [x] ?metaphlan-makdb
- [x] ?motus-downloaddb
- [x] ganon-buildcustom
- [ ] ?ganon-build
- [x] kmcp-compute
- [x] kmcp-index