1.1.0

hostile

Main tool: hostile

Code repository: https://github.com/bede/hostile

Basic information on how to use this tool:

• executable: |

usage: hostile [-h] [--version] {clean,mask,fetch} ...

positional arguments:
  {clean,mask,fetch}
    clean             Remove reads aligning to an index from fastq[.gz] input files
    mask              Mask reference genome against target genome(s)
    fetch             Download and cache indexes from object storage for use with hostile clean

options:
  -h, --help          show this help message and exit
  --version           show program's version number and exit

• help: hostile --help
• version: hostle --version
• description: |

Hostile accurately removes host sequences from short and long read (meta)genomes, consuming single-read or paired fastq input.

Full documentation: https://github.com/bede/hostile

Testing hostile analysis

# Downloading test dataset
wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R1.fastq.gz --no-check-certificate
wget https://github.com/bacterial-genomics/test-datasets/raw/assembly/test_data/test_miniburk_R2.fastq.gz --no-check-certificate

# Running hostile clean on test dataset
hostile clean --index /data/test/sars-cov-2/sars-cov-2 --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz