Metadata-Version: 2.1
Name: deepconsensus
Version: 0.1.0
Summary: DeepConsensus
Home-page: https://github.com/google/deepconsensus
Author: Google LLC
License: UNKNOWN
Keywords: bioinformatics
Platform: UNKNOWN
Requires-Python: >=3.6,<3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# DeepConsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific
Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

![DeepConsensus overview diagram](https://raw.githubusercontent.com/google/deepconsensus/main/docs/images/pipeline_figure.png)

## Installation

### From pip package

```bash
pip install deepconsensus==0.1.0
```

You can ignore errors regarding google-nucleus installation, such as `ERROR:
Failed building wheel for google-nucleus`.

### From source

```bash
git clone https://github.com/google/deepconsensus.git
cd deepconsensus
source install.sh
```

(Optional) After `source install.sh`, if you want to run all unit tests, you can
do:

```bash
./run_all_tests.sh
```

## Usage

See the [quick start](docs/quick_start.md).

## Where does DeepConsensus fit into my pipeline?

After a PacBio sequencing run, DeepConsensus is meant to be run on the CCS reads
and subreads to create new corrected reads in FASTQ format that can take the
place of the CCS reads for downstream analyses.

See the [quick start](docs/quick_start.md) for an example of inputs and outputs.

NOTE: This initial release of DeepConsensus (v0.1) is not yet optimized for
speed, and only runs on CPUs. We anticipate this version to be too slow for many
uses. We are now prioritizing speed improvements, which we anticipate can
achieve acceptable runtimes.

## Disclaimer

This is not an official Google product.

NOTE: the content of this research code repository (i) is not intended to be a
medical device; and (ii) is not intended for clinical use of any kind, including
but not limited to diagnosis or prognosis.


