Hostile accurately removes host sequences from short and long read (meta)genomes, consuming single or paired FASTQ from files or stdin. Batteries are included – a human reference genome is downloaded when run for the first time. Hostile is precise by default, removing an order of magnitude fewer microbial reads than existing approaches while removing >99.5% of real human reads from 1000 Genomes Project samples.

• Version: 2.0.0
• Added: March, 2025
• Link: https://github.com/bede/hostile

See versions that are available:

$ module avail hostile

Load one version into your environment and run it:

$ module load hostile/2.0.0
$ hostile

Notes from the sysadmin during installation.

$ sudo mkdir -p /export/apps/hostile/2.0.0
$ sudo chown aorth /export/apps/hostile/2.0.0
$ module load python/3.10
$ python3 -m venv /export/apps/hostile/2.0.0
$ source /export/apps/hostile/2.0.0/bin/activate
$ pip install -U pip setuptools wheel
$ pip install hostile==2.0.0
$ sudo chown -R root /export/apps/hostile/2.0.0

See the list of dependencies used in the Conda environment: https://github.com/bede/hostile/blob/main/environment.yml