IMPORTANT this repository is no longer being maintained. Onward development of the BAP is taking place at: https://github.com/zwets/cge-bap.
The KCRI CGE Bacterial Analysis Pipeline (BAP) is the standard analysis pipeline for bacterial genomics at Kilimanjaro Clinical Research Institute (KCRI). The BAP is developed in collaboration with the Centre for Genomic Epidemiology (CGE) at the Technical University of Danmark (DTU).
The BAP orchestrates a standard workflow that processes sequencing reads and/or contigs, and produces the following:
- Genome assembly (optional) (SKESA, Flye)
- Basic QC metrics over reads a/o contigs (fastq-stats, uf-stats)
- Species identification (KmerFinder, KCST)
- MLST (KCST, MLSTFinder)
- Resistance profiling (ResFinder, PointFinder, DisinfFinder)
- Plasmid detection and typing (PlasmidFinder, pMLST)
- Virulence gene finding (VirulenceFinder)
- Core genome MLST (optional) (cgMLSTFinder)
The BAP comes with sensible default settings and a standard workflow, but can be adjusted with command line parameters.
Since release 3.3.0, the BAP can process Illumina reads, Nanopore reads, or assembled contigs. You can pass it one of the following:
- A single FASTA file with (assembled) contigs
- A pair of Illumina paired-end reads files or a single Illumina reads file
- A single Nanopore reads file
The BAP generates a JSON file bap-results.json that integrates the detailed
output from all the services, and a tab-separated bap-summary.tsv with just
the most important results.
It also retains all raw output from the individual services that have run.
The BAP can do assembly, but doesn't do this by default. It will perform assembly only if either some service requires contigs as its input, or you explicitly instruct the BAP to do assembly (see below).
Note: Nanopore reads are likely to trigger the BAP to do assembly, because not all back-end services are ready for Nanopore reads, whereas most can process Illumina reads without the need to assemble first.
The BAP makes no effort to produce "polished" assemblies; use dedicated tools if that is your goal. The BAP invokes assemblers (currently SKESA for Illumina reads, Flye for Nanopore) with their recommended settings. Both (claim to) do a decent job on unprocessed raw reads.
Default run on a genome assembly:
BAP assembly.fna
Same but on paired-end Illumina reads:
BAP read_1.fq.gz read_2.fq.gz
Same but also produce the assembled genome:
BAP -t DEFAULT,assembly read_1.fq.gz read_2.fq.gz
The -t/--target parameter specifies the analyses the BAP must do.
When omitted, it has value DEFAULT, which implies these targets:
metrics, species, MLST, resistance, plasmids, virulence
(cgmlst is not run by default due to its long runtime).
Note how targets are 'logical' names for the tasks the BAP must do. The BAP will determine which services to involve, in what order, and what alternatives to try if a service fails.
See available targets:
BAP --list-targets
-> metrics species mlst resistance virulence plasmids ...
Perform only assembly and species typing (by omitting the DEFAULT target):
BAP -t assembly,species read_1.fq.gz read_2.fq.gz
Compute metrics only:
BAP -t metrics read_1.fq.gz read_2.fq.gz
Do the defaults but exclude metrics:
BAP -x metrics read_1.fq.gz read_2.fq.gz
Service parameters can be passed to individual services in the pipeline. For instance, to change ResFinder's identity and coverage thresholds:
BAP --rf-i=0.95 --rf-c=0.8 assembly.fna
For an overview of available parameters, use --help:
BAP --help
Call any of the backend services directly, not involving the BAP:
bap-container-run kmerfinder --help
bap-container-run SKESA --help
Run a terminal shell in the container:
bap-container-run
The BAP was developed to run on a moderately high-end Linux workstation (see history below). It is most easily installed in a Docker container.
The installation has two major steps: building the Docker image, and downloading the databases.
Test that Docker is installed
docker version
docker run hello-world
Clone and enter this repository
git clone https://github.com/kcri-tz/kcri-cge-bap.git
cd kcri-cge-bap
Download the backend services
ext/update-backends.sh
Build the kcri-cge-bap Docker image
./build.sh
# Or manually do what build.sh does:
#docker build -t kcri-cge-bap "." | tee build.log
Smoke test the container
# Run 'BAP --help' in the container, using the bin/BAP wrapper.
# (We set BAP_DB_DIR to a dummy as we have no databases yet)
BAP_DB_DIR=/tmp bin/BAP --help
Index the test databases
# This uses the kma_index and kcst indexers in the freshly built
# image to index test/databases/*:
scripts/index-databases.sh test/databases
Run on test data against the test databases:
# Test run BAP on an assembled sample genome
test/test-01-fa.sh
# Run BAP on a sample of paired-end reads
test/test-02-fq.sh
# Compute metrics over FASTA and FASTQ
test/test-03-metrics.sh
# Run BAP including assembly
test/test-04-asm.sh
If the tests above all end with with [OK], you are good to go. (Note
the test reads are just a small subset of a normal run, so the run output
for tests 02 and 03 is not representative.)
In the previous step we tested against the miniature test databases that come with this repository. In this step we install the real databases.
NOTE: The download can take a lot of time. The KmerFinder and cgMLST databases in particular are very large (~100GB). It is possible to run the BAP without these, but with loss of functionality.
Pick a location for the databases:
# Remember to set this BAP_DB_DIR in bin/bap-container-run
BAP_DB_DIR=/data/genomics/cge/db # KCRI path, replace by yours
Clone the CGE database repositories:
mkdir -p "$BAP_DB_DIR"
scripts/clone-databases.sh "$BAP_DB_DIR"
You now have databases for all services except KmerFinder and cgMLST. To download these (or a subset), follow the instructions in the repositories.
cd "$BAP_DB_DIR/kmerfinder"
less README.md # has instructions on download and installation
Run tests against the real databases (ignore failure "does not match expected output" as there may have been additions to the CGE databases):
# With BAP_DB_DIR pointing at the installed databases
test/test-04-fa-live.sh
test/test-05-fq-live.sh
If the tests succeeded, set BAP_DB_DIR in bin/bap-container-run to point
at the installed databases.
For convenience, add the bin directory to your PATH (edit your ~/.profile),
or copy or symlink the bin/BAP script in ~/.local/bin or ~/bin.
Once this is done (you may need to logout and login), BAP --help should work.
To upgrade to the latest BAP release:
git pull # pulls the current edge
git describe # check that it is not a WIP commit
git checkout x.y.z # otherwise pick latest stable release
ext/update-backends.sh # remember always do this _before_ building
./build.sh` # build and enjoy
To update the CGE databases
# Just rerun the installation script (with same DB_DIR)
scripts/clone-databases.sh DB_DIR
Updating any backend service can be done by changing its required version in
ext/backend-versions.config, then running:
ext/update-backends.sh
./build.sh
Always run tests after upgrading:
# Index the test databases (in the rare case they were upgraded)
scripts/index-databases.sh test/databases
# Runs the tests we ran above
test/run-all-tests.sh
The KCRI BAP evolved from the CGE BAP (citation below), the original code of
which is at https://bitbucket.org/genomicepidemiology/cge-tools-docker.git.
The KCRI version initially lived on the kcri branch in that repository, but
moved to its own project after development of the BAP master stopped.
The KCRI BAP was developed to run on modest hardware, independent of an HPC batch submission system. It ran at KCRI for several years on a cluster of four 8 core, 32GB Dell Precision M4700 laptop workstations.
As the BAP evolved, its workflow logic became unwieldy and was factored out
into a simple generic mechanism. That code is now in https://github.com/zwets/picoline
whereas all BAP-specifics (the workflow definitions and service shims) are
here in the src/kcri/bap package.
The next generation BAP "2.0" is under development at CGE, and is based on the NextFlow workflow control engine. We envisage migrating KCRI BAP to that foundation once it is operational.
For publications please cite the URL https://github.com/kcri-tz/kcri-cge-bap of this repository, and the paper on the original concept:
A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance. Martin Christen Frølund Thomsen, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Vanessa Jurtz, Mette Voldby Larsen, Henrik Hasman, Frank Møller Aarestrup, Ole Lund; PLoS One. 2016; 11(6): e0157718.
Refer to the individual tools invoked by the BAP for their preferred citations.
Copyright 2016-2019 Center for Genomic Epidemiology, Technical University of Denmark
Copyright 2018-2022 Kilimanjaro Clinical Research Institute, Tanzania
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.