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https://github.com/mbhall88/tbpore
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
https://github.com/mbhall88/tbpore
bioinformatics drug-resistance-prediction genomics mycobacterium-tuberculosis nanopore variant-calling
Last synced: 2 months ago
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Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
- Host: GitHub
- URL: https://github.com/mbhall88/tbpore
- Owner: mbhall88
- License: mit
- Created: 2021-11-25T06:33:42.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2023-10-11T03:52:01.000Z (about 1 year ago)
- Last Synced: 2024-05-03T02:08:43.040Z (8 months ago)
- Topics: bioinformatics, drug-resistance-prediction, genomics, mycobacterium-tuberculosis, nanopore, variant-calling
- Language: Python
- Homepage:
- Size: 3.3 MB
- Stars: 11
- Watchers: 7
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# TBpore
*Mycobacterium tuberculosis* genomic analysis from Nanopore sequencing data
[](https://github.com/mbhall88/tbpore/actions/workflows/ci.yaml)
[](https://codecov.io/gh/mbhall88/tbpore)
[](https://pypi.org/project/tbpore/)
[](https://opensource.org/licenses/MIT)
[](https://github.com/psf/black)
[TOC]: #
# Table of Contents
- [TBpore](#tbpore)
- [Table of Contents](#table-of-contents)
- [Synopsis](#synopsis)
- [Citation](#citation)
- [Installation](#installation)
- [conda](#conda)
- [pip](#pip)
- [Dependencies](#dependencies)
- [Container](#container)
- [`singularity`](#singularity)
- [`docker`](#docker)
- [Configuring the decontamination database index](#configuring-the-decontamination-database-index)
- [Performance](#performance)
- [`tbpore process`](#tbpore-process)
- [`tbpore cluster`](#tbpore-cluster)
- [Usage](#usage)
- [General usage](#general-usage)
- [process](#process)
- [cluster](#cluster)
- [download](#download)
## Synopsis
`tbpore` is a tool with two main goals.
First is to process Nanopore Mycobacterium tuberculosis sequencing data to describe
variants with respect to the
canonical TB strain H37Rv and predict antibiotic resistance (command `tbpore process`).
Variant description is done by decontaminating reads, calling variants with
[bcftools](https://github.com/samtools/bcftools) and filtering variants.
Antibiotic resistance is predicted
with [mykrobe](https://github.com/Mykrobe-tools/mykrobe).
Second, `tbpore` can be used to cluster TB samples based on their genotyping and a given
distance threshold (command
`tbpore cluster`).
## Citation
TBpore is a slimmed-down version of
the [full pipeline](https://github.com/mbhall88/head_to_head_pipeline) used
in our paper 👇
> Hall, M. B. et al. Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. *The Lancet Microbe* 0, (2022) doi: [10.1016/S2666-5247(22)00301-9][doi].
[doi]: https://doi.org/10.1016/S2666-5247(22)00301-9
## Installation
### conda
[](https://anaconda.org/bioconda/tbpore)
[](https://anaconda.org/bioconda/tbpore)
Prerequisite: [`conda`][conda] (and bioconda channel [correctly set up][channels])
```shell
$ conda install tbpore
```
### pip
The python components of `tbpore` are availble to install through [PyPI].
```shell
pip install tbpore
```
**However**, you will need to install the following dependencies, which cannot be
installed through PyPI.
#### Dependencies
* [`rasusa`](https://github.com/mbhall88/rasusa) version 2.x
* [`psdm`](https://github.com/mbhall88/psdm) version 0.1.x
* [`samtools`](https://github.com/samtools/samtools) version 1.13
* [`bcftools`](https://github.com/samtools/bcftools) version 1.13
* [`mykrobe`](https://github.com/Mykrobe-tools/mykrobe) version 0.12.x
* [`minimap2`](https://github.com/lh3/minimap2) version 2.22
* [`seqkit`](https://bioinf.shenwei.me/seqkit/) version 2.x
* [`nanoq`](https://github.com/esteinig/nanoq) version 0.9.x
We make no guarentees about the performance of `tbpore` with versions other than those
specified above. In particular, the `bcftools` version is very important. The latest
versions of the other dependencies can likely be used.
### Container
Docker images are provided through biocontainers.
#### `singularity`
Prerequisite: [`singularity`][singularity]
```shell
$ URI="docker://quay.io/biocontainers/tbpore:"
$ singularity exec "$URI" tbpore --help
```
see [here][tags] for valid values for ``.
#### `docker`
[](https://quay.io/repository/biocontainers/tbpore)
Prerequisite: [Docker]
```shell
$ docker pull quay.io/biocontainers/tbpore:
$ docker run quay.io/biocontainers/tbpore: tbpore --help
```
see [here][tags] for valid values for ``.
## Configuring the decontamination database index
After installing TBpore, you will need to download the decontamination database index.
```
$ tbpore download
```
By default, this will download the index
to `${HOME}/.tbpore/decontamination_db/remove_contam.map-ont.mmi`, as this is the
default location `tbpore process` will search for.
If you prefer to download the index to another location, this can be done with
```
$ tbpore download -o other/location/db.mmi
```
Keep in mind, if you specify a non-default location, you will need to use the `--db`
option when running `tbpore process`.
## Performance
### `tbpore process`
Benchmarked on 151 TB ONT samples with 1 thread:
* Runtime: `2103`s avg, `4048`s max (s = seconds);
* RAM: `12.4`GB avg, `13.1`GB max (GB = Gigabytes);
### `tbpore cluster`
Clustering 151 TB ONT samples:
* Runtime: `286`s;
* RAM: `<1`GB;
## Usage
### General usage
```
Usage: tbpore [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
-V, --version Show the version and exit.
-v, --verbose Turns on debug-level logger. Option is mutually exclusive
with quiet.
-q, --quiet Turns off all logging except errors. Option is mutually
exclusive with verbose.
Commands:
cluster Cluster consensus sequences
download Download and validate the decontamination database
process Single-sample TB genomic analysis from Nanopore sequencing data
```
### process
```
Usage: tbpore process [OPTIONS] [INPUTS]...
Single-sample TB genomic analysis from Nanopore sequencing data
INPUTS: Fastq file(s) and/or a directory containing fastq files. All files
will be joined into a single fastq file, so ensure they're all part of the
same sample/isolate.
Options:
-h, --help Show this message and exit.
-r, --recursive Recursively search INPUTS for fastq files
-S, --name TEXT Name of the sample. By default, will use the
first INPUT file with fastq extensions
removed
-A, --report_all_mykrobe_calls Report all mykrobe calls (turn on flag -A,
--report_all_calls when calling mykrobe)
--db PATH Path to the decontaminaton database
[default: /home/mihall/.tbpore/decontaminati
on_db/remove_contam.map-ont.mmi]
-m, --metadata PATH Path to the decontaminaton database metadata
file [default: /data/scratch/projects/punim
1703/tmp/outliers/tbpore/data/decontaminatio
n_db/remove_contam.tsv.gz]
-c, --coverage INTEGER Depth of coverage to subsample to. Use 0 to
disable
-o, --outdir DIRECTORY Directory to place output files [default:
.]
--tmp DIRECTORY Specify where to write all (tbpore)
temporary files. [default: /.tbpore]
-t, --threads INTEGER Number of threads to use in multithreaded
tools [default: 1]
-d, --cleanup / -D, --no-cleanup
Remove all temporary files on *successful*
completion [default: no-cleanup]
--cache DIRECTORY Path to use for the cache [default:
/home/mihall/.cache]
```
### cluster
```
Usage: tbpore cluster [OPTIONS] [INPUTS]...
Cluster consensus sequences
Preferably input consensus sequences previously generated with tbpore
process.
INPUTS: Two or more consensus fasta sequences. Use glob patterns to input
several easily (e.g. output/sample_*/*.consensus.fa).
Options:
-h, --help Show this message and exit.
-T, --threshold INTEGER Clustering threshold [default: 6]
-o, --outdir DIRECTORY Directory to place output files [default:
.]
--tmp DIRECTORY Specify where to write all (tbpore)
temporary files. [default: /.tbpore]
-t, --threads INTEGER Number of threads to use in multithreaded
tools [default: 1]
-d, --cleanup / -D, --no-cleanup
Remove all temporary files on *successful*
completion [default: no-cleanup]
--cache DIRECTORY Path to use for the cache [default:
/Users/michaelhall/.cache]
```
### download
```
Usage: tbpore download [OPTIONS]
Download and validate the decontamination database
Options:
-h, --help Show this message and exit.
-o, --output PATH Download database to a specified filepath [default: ${HOME}/
.tbpore/decontamination_db/remove_contam.map-ont.mmi]
-f, --force Force overwrite if the database already exists
```
[channels]: https://bioconda.github.io/#usage
[conda]: https://docs.conda.io/projects/conda/en/latest/user-guide/install/
[PyPI]: https://pypi.org/project/tbpore/
[singularity]: https://sylabs.io/guides/3.6/user-guide/quick_start.html#quick-installation-steps
[tags]: https://quay.io/repository/biocontainers/tbpore?tab=tags
[Docker]: https://docs.docker.com/v17.12/install/