Description

Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1' ]

fasta (file)

The genome file that is used to generate everything

*.{fsa,fa,fasta}

pass_list (file)

A list of intact LTR-RTs generated by LTR_retriever

*.pass.list

annotation_out (file)

RepeatMasker annotation of all LTR sequences in the genome

*.out

monoploid_seqs (file)

This parameter is mainly for ployploid genomes. User provides a list of
sequence names that represent a monoploid (1x). LAI will be calculated only
on these sequences if provided.

*.txt

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

log (file)

Log from LAI

*.LAI.log

lai_out (file)

Output file from LAI if LAI is able to estimate the index from the inputs

*.LAI.out

versions (file)

File containing software versions

versions.yml

Tools

lai
GPL v3

Assessing genome assembly quality using the LTR Assembly Index (LAI)