Description

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

Input

Name
Description
Pattern

0 ()

1 ()

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
Description
Pattern

0 ()

0 ()

0 ()

Tools

lai Documentation

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

doi: 10.1093/nar/gky730License: GPL v3
Authors