Commit d42eeabb authored by Overduin, Sam's avatar Overduin, Sam
Browse files

Update README.md

parent 860c5029
......@@ -36,12 +36,14 @@ pip3 install ete3
The first time the annotation script is run, it will download the NCBI taxonomy database to your $HOME. Keep in mind this will increase the running time the first time it is run.
Run the annotation script with:
Run the annotation script from the source directory with:
```bash
chmod +x scripts/append_taxatree_to_reads.py
scripts/append_taxatree_to_reads.py -i $input_reads.fastq.gz -k $kraken_out_file -o $reads_with_taxatree.fastq.gz
```
If you have built & installed taxaSPAdes or are using the prebuilt binaries, you can find the script at ```$install_dir/bin/append_taxatree_to_reads.py```
Optional options are:
```--main_ranks or -m```
Flag to keep only major ranks (domain, kingdom, phylum, class, order, family, genus, species) when annotating the taxonomy.
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment