Using Assembled Contig Data with Melon: Compatibility and Guidelines

xinehc / melon

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

MIT License

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Using Assembled Contig Data with Melon: Compatibility and Guidelines #3

Open ystone1101 opened 2 months ago

ystone1101 commented 2 months ago

Hi,

Does Melon accept assembled contig data produced from short-read sequencing data using assemblers (e.g., MEGAHIT, metaSPAdes...) ?

xinehc commented 2 months ago

Hi,

Melon is a read-based taxonomic profiler so it does not work with contigs.

ystone1101 commented 2 months ago

Hi, Thank you for the clarification.

muhit-emon commented 3 weeks ago

Hi,

Does Melon work with assembled contigs from long-read data using assemblers like Canu, MetaFlye?

xinehc commented 3 weeks ago

Hi,

no, the main usage of Melon is to estimate the genome copies of different species in a metagenomic sample. Since assembled contigs do not have the coverage information Melon cannot handle them.