dRep

Rapid and accurate comparison and de-replication of microbial genomes

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File naming

The dRep format is a special case that requires two files:

• Cdb.csv
• Wdb.csv

Their names have to be exactly as above.

File format

tip

For more information on the dRep output files, visit the dRep documentation.

Cdb.tsv

This file informs the cluster of every MAG.

The file must follow the Tab Separated Values (TSV). It must have columns representing the following data, in that order and with a header:

Column name	Column obligatoriness	Data type	Data nullability
genome	Mandatory	String	Not nullable
secondary_cluster	Mandatory	String	Nullable
threshold	Optional (ignored)	N/A	N/A
cluster_method	Optional (ignored)	N/A	N/A
comparison_algorithm	Optional (ignored)	N/A	N/A
primary_cluster	Optional (ignored)	N/A	N/A

Wdb.tsv

This file informs the "winners" (i.e. best representatives) of each cluster.

The file must follow the Tab Separated Values (TSV). It must have columns representing the following data, in that order and with a header:

Column name	Column obligatoriness	Data type	Data nullability
genome	Mandatory	String	Not nullable
score	Optional (ignored)	N/A	N/A
cluster	Optional (ignored)	N/A	N/A

Mapping to database

DrepDirectory

Original data	DrepDirectory field
dRep directory path	path 1

DrepEntry

Original data	DrepEntry field
genome column of Wdb.csv	winner 2
genome column of Cdb.csv	genome_name
secondary_cluster column of Cdb.csv	genome_cluster_name

Footnotes

1. This is the path to the directory that contains both Cdb.csv and Wdb.csv. ↩

2. MAGs whose names are in Wdb.csv are the winners of theirs clusters. ↩