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pip --extra-index-url
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iiSeymour committed Sep 5, 2022
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[![py38](https://img.shields.io/badge/python-3.8-brightgreen.svg)](https://img.shields.io/badge/python-3.8-brightgreen.svg)
[![py39](https://img.shields.io/badge/python-3.9-brightgreen.svg)](https://img.shields.io/badge/python-3.9-brightgreen.svg)
[![py310](https://img.shields.io/badge/python-3.10-brightgreen.svg)](https://img.shields.io/badge/python-3.10-brightgreen.svg)
[![cu102](https://img.shields.io/badge/cuda-10.2-blue.svg)](https://img.shields.io/badge/cuda-10.2-blue.svg)
[![cu113](https://img.shields.io/badge/cuda-11.3-blue.svg)](https://img.shields.io/badge/cuda-11.3-blue.svg)

A PyTorch Basecaller for Oxford Nanopore Reads.
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$ bonito basecaller [email protected] /data/reads > basecalls.bam
```

By default `pip` will install `torch` which is build against CUDA 10.2. For CUDA 11.3 builds run:

```
$ pip install --extra-index-url https://download.pytorch.org/whl/cu113 ont-bonito
```

Bonito supports writing aligned/unaligned `{fastq, sam, bam, cram}`.

```bash
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