millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 06:59:54 +00:00
Code Issues Releases Packages Activity

Add new line in the description of custom file

Browse source
This commit is contained in:
Sofia Stamouli 2023-01-19 13:44:10 +01:00 committed by GitHub
parent 4dcf8c0b02
commit 7d4035d4c7
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 6 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

11
docs/usage.md
View file

@ -470,11 +470,12 @@ You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.sht
Centrifuge allows the user to [build custom databases](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database). The user should download taxonomy files, make custom `seqid2taxid.map` and combine the fasta files together. You need four components: a tab-separated file mapping sequence IDs to taxonomy IDs (`--conversion-table`), a \t|\t-separated file mapping taxonomy IDs to their parents and rank, up to the root of the tree (`--taxonomy-tree`), a '|'-separated file mapping taxonomy IDs to a name (`--name-table`) and the reference sequences.
An example of custom `seqid2taxid.map`:
NC_001133.9 4392
NC_012920.1 9606
NC_001134.8 4392
NC_001135.5 4392
```
NC_001133.9 4392
NC_012920.1 9606
NC_001134.8 4392
NC_001135.5 4392
```
```bash
centrifuge-download -o taxonomy taxonomy