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TBpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Python CI codecov PyPI PyPI - Python Version License: MIT Code style: black

Table of Contents

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 and filtering variants. Antibiotic resistance is predicted with 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 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.

Installation

conda

Conda (channel only) bioconda version Conda

Prerequisite: conda (and bioconda channel correctly set up)

$ conda install tbpore

pip

PyPI PyPI - Python Version

The python components of tbpore are availble to install through PyPI.

pip install tbpore

However, you will need to install the following dependencies, which cannot be installed through PyPI.

Dependencies

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

$ URI="docker://quay.io/biocontainers/tbpore:<tag>"
$ singularity exec "$URI" tbpore --help

see here for valid values for <tag>.

docker

Docker Repository on Quay

Prerequisite: Docker

$ docker pull quay.io/biocontainers/tbpore:<tag>
$ docker run quay.io/biocontainers/tbpore:<tag> tbpore --help

see here for valid values for <tag>.

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: 2103s avg, 4048s max (s = seconds);
  • RAM: 12.4GB avg, 13.1GB max (GB = Gigabytes);

tbpore cluster

Clustering 151 TB ONT samples:

  • Runtime: 286s;
  • RAM: <1GB;

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: <outdir>/.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: <outdir>/.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