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# Hostile

Hostile removes host sequences from short and long reads, consuming paired or unpaired `fastq[.gz]` input. 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](https://log.bede.im/2023/08/29/precise-host-read-removal.html#evaluating-accuracy) than existing approaches while removing >99.5% of real human reads from 1000 Genomes Project samples. For ultimate precision, a prebuilt masked reference can be downloaded, or a new one created for chosen target organisms. Read headers can be replaced with integers (using `--rename`) for privacy and smaller FASTQs. Heavy lifting is done with fast existing tools (Minimap2/Bowtie2 and Samtools). Bowtie2 is the default aligner for short (paired) reads while Minimap2 is default aligner for long reads. In benchmarks, bacterial Illumina reads were decontaminated at 32Mbp/s (210k reads/sec) and bacterial ONT reads at 22Mbp/s, using 8 alignment threads. Further information and benchmarks can be found in the [paper](https://doi.org/10.1093/bioinformatics/btad728) and [blog post](https://log.bede.im/2023/08/29/precise-host-read-removal.html). Please open an issue, [tweet](https://twitter.com/beconsta), [toot](https://mstdn.science/@bede) or email me to report problems or suggest improvements.
Hostile removes host sequences from short and long reads, consuming paired or unpaired `fastq[.gz]` input. 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](https://log.bede.im/2023/08/29/precise-host-read-removal.html#evaluating-accuracy) than existing approaches while removing >99.5% of real human reads from 1000 Genomes Project samples. For maximum precision, masked reference genomes can be downloaded or built for target genomes. Read headers can be replaced with integers (using `--rename`) for privacy and smaller FASTQs. Heavy lifting is done with fast existing tools (Minimap2/Bowtie2 and Samtools). Bowtie2 is the default aligner for short (paired) reads while Minimap2 is default aligner for long reads. In benchmarks, bacterial Illumina reads were decontaminated at 32Mbp/s (210k reads/sec) and bacterial ONT reads at 22Mbp/s, using 8 alignment threads. Further information and benchmarks can be found in the [paper](https://doi.org/10.1093/bioinformatics/btad728) and [blog post](https://log.bede.im/2023/08/29/precise-host-read-removal.html). Please open an issue to report problems [or](mailto:[email protected]) [otherwise](https://twitter.com/beconsta) [reach](https://bsky.app/profile/bedec.bsky.social) [out](https://mstdn.science/@bede) for help, advice etc.



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