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Update README.md
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GaetanBenoitDev authored Jan 9, 2024
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Developper: Gaëtan Benoit
Contact: gaetanbenoitdev at gmail dot com

## Notes on input data (PacBio and Nanopore)

- MetaMDBG has been developped using **PacBio HiFi** data.
- MetaMDBG will not work on raw **Nanopore** reads, but error rate is improving quickly, it might work on duplex data in the future. Currently, you have to polish the reads first. For that, you can use [VeChat](https://github.com/HaploKit/vechat) (using Nanopore reads only), or [Ratatosk](https://github.com/DecodeGenetics/Ratatosk) (Using Nanopore + Illumina short-reads).

## Installation

### Conda
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MetaMDBG will generate polished contigs in outputDir ("contigs.fasta.gz").

## Input data (PacBio and Nanopore)

- MetaMDBG has been developped using **PacBio HiFi** data.
- MetaMDBG will not work on raw **Nanopore** reads, but error rate is improving quickly, it might work on duplex data in the future. Currently, you have to polish the reads first. For that, you can use [VeChat](https://github.com/HaploKit/vechat) (using Nanopore reads only), or [Ratatosk](https://github.com/DecodeGenetics/Ratatosk) (using Nanopore + Illumina short-reads).

## Contig information
Contig information, such as whether it is circular or not, are contained in contig headers in the resulting assembly file.
Examples:
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