1 unstable release
| 0.1.0 | Dec 14, 2023 |
|---|
#148 in Biology
32KB
445 lines
NoHuman
👤➡️🚫 Remove human reads from a sequencing run 👤➡️🚫
nohuman removes human reads from sequencing reads by classifying them with kraken2 against a custom database built from all of the genomes in the Human Pangenome Reference Consortium's (HPRC) first draft human pangenome reference. It can take any type of sequencing technology. Read more about the development of this method here.
Install
Conda (recommended)
$ conda install -c bioconda nohuman
Precompiled binary
Note: you will need to install kraken2 yourself using this install method.
curl -sSL nohuman.mbh.sh | sh
# or with wget
wget -nv -O - nohuman.mbh.sh | sh
You can also pass options to the script like so
$ curl -sSL nohuman.mbh.sh | sh -s -- --help
install.sh [option]
Fetch and install the latest version of nohuman, if nohuman is already
installed it will be updated to the latest version.
Options
-V, --verbose
Enable verbose output for the installer
-f, -y, --force, --yes
Skip the confirmation prompt during installation
-p, --platform
Override the platform identified by the installer [default: apple-darwin]
-b, --bin-dir
Override the bin installation directory [default: /usr/local/bin]
-a, --arch
Override the architecture identified by the installer [default: x86_64]
-B, --base-url
Override the base URL used for downloading releases [default: https://github.com/mbhall88/nohuman/releases]
-h, --help
Display this help message
Cargo
Note: you will need to install kraken2 yourself using this install method.
$ cargo install nohuman
Container
Docker images are hosted at quay.io.
singularity
Prerequisite: singularity
$ URI="docker://quay.io/mbhall88/nohuman"
$ singularity exec "$URI" nohuman --help
The above will use the latest version. If you want to specify a version then use a tag (or commit) like so.
$ VERSION="0.1.0"
$ URI="docker://quay.io/mbhall88/nohuman:${VERSION}"
docker
Prerequisite: docker
$ docker pull quay.io/mbhall88/nohuman
$ docker run quay.io/mbhall88/nohuman nohuman --help
You can find all the available tags on the quay.io repository.
Build from source
Note: you will need to install kraken2 yourself using this install method.
$ git clone https://github.com/mbhall88/nohuman.git
$ cd nohuman
$ cargo build --release
$ target/release/nohuman -h
Usage
Download the database
$ nohuman -d
by default, this will place the database in $HOME/.nohuman/db. If you want to download it somewhere else, use the --db option.
Check dependecies are available
$ nohuman -c
[2023-12-14T04:10:46Z INFO ] All dependencies are available
Remove human reads
$ nohuman -t 4 in.fq
this will pass 4 threads to kraken2 and output the clean reads as in.nohuman.fq.
You can specify where to write the output file with -o
$ nohuman -t 4 -o clean.fq in.fq
If you have paired-end Illumina reads
$ nohuman -t 4 in_1.fq in_2.fq
or to specify a different path for the output
$ nohuman -t 4 --out1 clean_1.fq --out2 clean_2.fq in_1.fq in_2.fq
Note: output will always be uncompressed, even if compressed input is provided.
$ nohuman -h
Remove human reads from a sequencing run
Usage: nohuman [OPTIONS] [INPUT]...
Arguments:
[INPUT]... Input file(s) to remove human reads from
Options:
-o, --out1 <OUTPUT_1> First output file
-O, --out2 <OUTPUT_2> Second output file - if two input files given
-c, --check Check that all required dependencies are available
-d, --download Download the database
-D, --db <PATH> Path to the database [default: /home/mihall/.nohuman/db]
-t, --threads <INT> Number of threads to use in kraken2 [default: 1]
-v, --verbose Set the logging level to verbose
-h, --help Print help (see more with '--help')
-V, --version Print version
Full usage
$nohuman --help
Remove human reads from a sequencing run
Usage: nohuman [OPTIONS] [INPUT]...
Arguments:
[INPUT]...
Input file(s) to remove human reads from
Options:
-o, --out1 <OUTPUT_1>
First output file.
Defaults to the name of the first input file with the suffix "nohuman" appended. e.g. "input_1.fastq.gz" -> "input_1.nohuman.fq". NOTE: kraken2 output cannot be compressed, so the output will always be uncompressed.
-O, --out2 <OUTPUT_2>
Second output file - if two input files given.
Defaults to the name of the first input file with the suffix "nohuman" appended. e.g. "input_2.fastq.gz" -> "input_2.nohuman.fq". NOTE: kraken2 output cannot be compressed, so the output will always be uncompressed.
-c, --check
Check that all required dependencies are available
-d, --download
Download the database
-D, --db <PATH>
Path to the database
[default: /home/mihall/.nohuman/db]
-t, --threads <INT>
Number of threads to use in kraken2
[default: 1]
-v, --verbose
Set the logging level to verbose
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version
Alternates
Hostile is an alignment-based approach that performs well. It take longer and uses more memory than the nohuman kraken approach, but has slightly better accuracy for Illumina data. See the paper for more details and for other alternate approaches.
Cite
Hall, Michael B., and Lachlan J. M. Coin. “Pangenome Databases Provide Superior Host Removal and Mycobacteria Classification from Clinical Metagenomic Data.” bioRxiv, September 19, 2023. https://doi.org/10.1101/2023.09.18.558339.
@misc{hall_pangenome_2023,
title = {Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data},
url = {https://www.biorxiv.org/content/10.1101/2023.09.18.558339v3},
doi = {10.1101/2023.09.18.558339},
language = {en},
urldate = {2023-09-20},
publisher = {bioRxiv},
author = {Hall, Michael B. and Coin, Lachlan J. M.},
month = sep,
year = {2023},
}
Dependencies
~17–33MB
~532K SLoC