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


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:
chmod +x scripts/
scripts/ -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/```
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.
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