Description

Define the mappability of a reference

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

index (file)

The index created with gem-indexer from the reference FASTA

*.gem

read_length (integer)

The read length to define the mappability of

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

map (file)

The resulting mappability file

*.mappability

Tools

gem2
Custom

GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.