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{:bash}

:map

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

fasta{:bash}

:file

The genome file that is used to generate everything

*.{fsa,fa,fasta}

pass_list{:bash}

:file

A list of intact LTR-RTs generated by LTR_retriever

*.pass.list

annotation_out{:bash}

:file

RepeatMasker annotation of all LTR sequences in the genome

*.out

monoploid_seqs{:bash}

: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

log{:bash}

meta{:bash}

:map

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

*.LAI.log{:bash}

:file

Log from LAI

*.LAI.log

lai_out{:bash}

meta{:bash}

:map

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

*.LAI.out{:bash}

:file

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

*.LAI.out

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

lai
GPL v3

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

github.com/oushujun/LTR_retriever 10.1093/nar/gky730
maintainer
Github user GallVp
get in touch
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