Run some read taxonomic classifiers on multiple samples
- conda and/or mamba
- snakemake > 6.0
Manually downloaded using the information below.
| Tool | Name | Description | Date created | Direct Link | Ref |
|---|---|---|---|---|---|
| centrifuge | nt | NCBI: nucleotide non-redundant sequences | March 3 2018 | https://genome-idx.s3.amazonaws.com/centrifuge/nt_2018_3_3.tar.gz | https://benlangmead.github.io/aws-indexes/ |
| kraken2 | PlusPf | archea,bacteria,viral,plasmid,human,UniVec_core, protozoa, fungi | May 5 2017 | https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_20210517.tar.gz | https://benlangmead.github.io/aws-indexes/ |
| kaiju | nr_euk | arahaea, bacteria, viruses, fungi, microbial eukaryotes | May 20 2020 | https://kaiju.binf.ku.dk/database/kaiju_db_nr_euk_2021-02-24.tgz | https://kaiju.binf.ku.dk/server |
For mgx users these are on mgx/programs/tool_name
Fill in the values of the config file as appropriate for your setup.
The samplesheet should point to a 3-column tsv file with columns
sample_id: A unique sample identifierR1: Path to R1 for that sampleR2: Path to R2 for that sample
Only paired-end data are supported for now.
$ snakemake -p -j24 --use-conda --conda-frontend mamba