Using Assembled Contig Data with Melon: Compatibility and Guidelines

[ystone1101]

Hi,

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

[xinehc]

Hi,

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

[ystone1101]

Hi, Thank you for the clarification.

[muhit-emon]

Hi,

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

[xinehc]

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.

However, it may be used for a rough quality assessment & quick taxonomic classification of MAGs, for example:

melon GCF_900232105.1.fa -d database -o .

INFO: Estimating genome copies ...
INFO: ... found 1.0 copies of genomes (bacteria: 1.0; archaea: 0).
INFO: Assigning taxonomy ...
INFO: Reassigning taxonomy ...                                                                                    
INFO: ... found 1 unique species (bacteria: 1; archaea: 0).
INFO: Done.

If all the eight marker genes are found, the estimated genome copy should be 1.0.

cat GCF_900232105.1_genomic.tsv

...species                       copy     abundance       identity
...Kuenenia stuttgartiensis_A    1.000    1.000000e+00    1.0000/1.0000

If the MAG is present in the reference database (e.g. GTDB), the estimated identity should be 1.0 or very close to it.