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README.md

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[**Flye**](https://github.com/fenderglass/Flye) is a long-read assembler based on the de Bruijn graph approach. [**metaFlye**](https://www.nature.com/articles/s41592-020-00971-x) is the dedicated metagenomic assembler of Flye. Use metaFlye (Flye in metagenomics mode) software to assemble long reads into contigs. A sample command is given below.
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```
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flye --meta --pacbio-raw reads.fasta -g metagenome_size --out-dir /path/output_folder --threads 16
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flye --meta --pacbio-raw reads.fasta --genome-size estimated_metagenome_size --out-dir /path/output_folder --threads 16
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```
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Next, you have to bin the resulting contigs using an existing contig-binning tool. We have used the following tools with their commands for the experiments.

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