Kodoja takes the raw data (either fasta or fastq) and uses Kraken, a k-mer-based tool, and Kaiju, which used the Burrows–Wheeler transform, to detect viral sequences in RNA-seq or sRNA-seq data.
There are three main scripts:
kodoja_search.py- classify RNA-seq data.kodoja_build.py- download viral/host genomes and create new Kraken and Kaiju databases.kodoja_retrieve.py- pull out sequences of interest fromkodoja_search.pyresults file.
Python files diagnostic_modules.py and database_modules.py contain the fuctions called by kodoja_search.py and kodoja_build.py, and are not intended for public use.
The .sh files are example scripts for submission to an SGE cluster.
For a examples of how to run the code please see the wiki page: https://github.com/abaizan/kodoja/wiki/Kodoja-Manual
Additionally, for those of you using the Galaxy web-platform for running bioinformatics analysis from your web-browser, we have provided a Galaxy Wrapper for Kodoja available to install from the Galaxy Tool Shed.
Please cite the following manuscript for Kodoja:
Amanda Baizan-Edge et al. (2019), Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data, Journal of General Virology https://doi.org/10.1099/jgv.0.001210
Kodoja is released under the MIT licence, see file LICENSE.txt for details.
The lower versions listed were those used in the initial development and/or local testing of Kodoja. Later updates will likely work unless the tool makes a backward incompatible change.
- FastQC v0.11.5
- Trimmomatic v0.36
- Kraken v1.0
- Kaiju v1.5.0
Python packages:
- numpy v1.9
- biopython v1.67
- pandas v0.14
- ncbi-genome-download v0.2.6
You can use Python 2.7 or Python 3, specifically Kodoja has been tested on Python 3.6.
A conda package has been prepared on the BioConda channel which will install Kodoja and the dependencies, all with just:
$ conda install -c bioconda kodoja
For manual installation, you must install all the dependencies by hand and then add the main
scripts folder to your $PATH so that you can run kodoja_search.py etc at the command
line.
You can use kodoja_build.py to make your own databses, or download the
pre-built database as described here.
The kodojaDB v1.0 was released Sept 2018 under the CC-BY 4.0 license. It can be downloaded and cited as https://doi.org/10.5281/zenodo.1406071 (where the metadata describes how it was made). We suggest you install it as follows:
$ cd /mnt/shared/data/
$ mkdir kodojaDB_v1.0
$ cd kodojaDB_v1.0
$ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz
$ tar -zxvf kodojaDB_v1.0.tar.gzYou would then use this with kodoja_search.py as follows:
$ kodoja_search.py --kraken_db /mnt/shared/data/kodojaDB_v1.0/krakenDB \
--kaiju_db /mnt/shared/data/kodojaDB_v1.0/kaijuDB \
...IMPORTANT: do not put original data in the output directory when executing kodoja_search!
--read1- path to the single-end or first paired-end file (required)--read2- path to second paired-end file (default=False)--data_format- specify the file-type for file1 ("fasta" or "fastq" - default='fastq')--output_dir- path to the results folder (required)--threads- number of threads on cluster (default=1)--host_subset- tax id of host. Use this is a host genome was added to the databases and you do not wish to see the number of reads classifed to this group in the final table
--kraken_db- path to kraken database (required)--kraken_quick- Quick operation mode of Kraken, where instead of querying all k-mers in the database, it stops at nth k-mer hit preload (default=False)
--kaiju_db- path to kaiju database, nodes.dmp and names.dmp files (required)--kaiju_minlen- minimun required fragment length length (default=15)--kaiju_mismatch- number of mismatches allowed by kaiju (default=1)--kaiju_score- minimum required match if mismatches introduced (default=85)
Set parameter for kaiju:
-x - used to enable filtering of query sequences
containing low-complexity regions by using the SEG algorithm from the blast+
package. Enabling this option is always recommended in order to avoid false
positive matches caused by spurious matches due to simple repeat patterns or
other sequencing noise.
--trim_minlen- minimum length read after trimming (default=50)--trim_adapt- fasta file with Illumina adaptor sequences to allow trimming (default=False)
Set parameters for trimmomatic
ILUMINACLIP 2:30:10 (seed mismatches:palindrome threshold:simple clip threshold) -
seedMismatches specifies the maximum mismatch count which will still allow a full match to be performed,
palindromeClipThreshold specifies how accurate the match between the two 'adapter ligated',
reads must be for PE palindrome read alignment,
simpleClipThreshold: specifies how accurate the match between
any adapter etc. sequence must be against a read.
LEADING:20 - Specifies the minimum quality required to keep a base
TRAILING:20 - Specifies the minimum quality required to keep a base
--output_dir- Output directory path where kraken and kaiju databases will be written, required')--threads- number of threads on cluster (default=1)--host- NCBI tax id for the host genome to be downloaded from refseq and added to the databases(default=False)--extra_files- List of file paths (default=False)--extra_taxids- List of tax ids corresponding to extra files (default=False)--all_viruses- Build databases with viruses from all hosts--db_tag- Suffix for databases (default=none)
--kraken_kmer- Kraken kmer size type=int, (default=31)--kraken_minimizer- Kraken minimizer size (default=15)
--download_parallel- number of genomes to download in parallel (default=4)--no_download- Genomes have already been downloaded and are in output folder (default=False)
--file_dir- Path to directory of kodoja_search results (required)--user_format- Sequence data format (default=fastq)--read1- Path to read 1 file (required)--read2- Path to read 2 file--taxID- Virus tax ID for subsetting (default: All viral sequences)--genus- Include sequences classified at the genus level in subset file--stringent- Only subset sequences identified to same virus by both tools
| Version | Date | Notes |
|---|---|---|
| 0.0.10 | 2018-08-16 | - Link to the online manual from command line help |
- Support Kaiju v1.7.0 (mkbwt now has a prefix) |
||
| 0.0.9 | 2018-10-16 | - Fix v0.0.8 regression in kodoja_retrieve.py |
| 0.0.8 | 2018-09-14 | - Output read ID not title in kraken_VRL.txt |
- Omit /1 and /2 suffixes in kraken_VRL.txt |
||
| 0.0.7 | 2018-09-07 | - Document installing prebuilt database from Zenodo |
| - Optimise sorting of pandas dataframes | ||
| - Zero not blank in cols 6 and 7 of virus_table.txt | ||
| - Automated testing of pinned & latest dependencies | ||
| 0.0.6 | 2018-09-04 | - Python 3 fix for kodoja_retrieve.py |
- Automated testing of kodoja_retrieve.py |
||
| - Also test paired reads without /1 and /2 suffixes | ||
| 0.0.5 | 2018-08-29 | - Refactor logging in kodoja_search.py |
| - Top level error handling, with logging in search | ||
- dictionary changed size during iteration bug |
||
| 0.0.4 | 2018-08-22 | - Code style updates (no functional changes) |
| - Provide cut-down NCBI taxonomy for tests cases | ||
| - Additional database build testing | ||
| - Downloads virus files with HTTPS rather than FTP | ||
| 0.0.3 | 2018-02-22 | - Include genus level counts in search results |
| - Simplify internal renaming of sequencing reads | ||
| 0.0.2 | 2018-01-22 | - Now tested under Python 3.6 as well as Python 2.7 |
| 0.0.1 | 2018-01-15 | - Initial release for BioConda packaging |
Kodoja is on GitHub, and has auotmated testing running on TravisCI, see special
file .travis.yml and webpage https://travis-ci.org/abaizan/kodoja/builds
for details.
The release process includes:
- Update version in
diagnosticTool_scripts/diagnostic_modules.py. - Update release history in this
README.mdfile. - Commit changes.
- Tag the commit with
git tag kodoja-vX.Y.Z - Push commits and tags to github with
git push origin master --tags - Submit a pull request to BioConda to update the package, which usally
just means bumping the version and updating the checksum in
meta.yaml: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/kodoja