Main tool: hostile
Code repository: https://github.com/bede/hostile
Additional tools:
- samtools 1.21
- minimap2 2.28
- bowtie2 2.5.1
- bedtools 2.31.1
Basic information on how to use this tool:
- executable: hostile
- help:--help
- version: --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
All hostile test files and references are included at /hostile/tests
# 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 /hostile/test/sars-cov-2/sars-cov-2 --fastq1 test_miniburk_R1.fastq.gz --fastq2 test_miniburk_R2.fastq.gz