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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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LAI for Big Genome #129

Closed pxxiao-hz closed 2 years ago

pxxiao-hz commented 2 years ago

Hi, @oushujun

For big genomes, can I split genome to run this pipeline to get the LAI? In this way, it's faster than the whole genome.

Best wishes!

oushujun commented 2 years ago

You may split the genome to get the full list of intact LTR and all LTR faster. It's recommended to run LAI on the full ploidy, otherwise it could not represent the genome. You need to split a polyploid genome based on subgenomes or haplotype to run LAI, otherwise it will underestimate the score.

Shujun

On Thu, Jul 21, 2022 at 9:55 PM pxxiao-hz @.***> wrote:

Hi, @oushujun https://github.com/oushujun

For big genomes, can I split genome to run this pipeline to get the LAI? In this way, it's faster than the whole genome.

Best wishes!

— Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/129, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NF3KAUQR3CZD67QXADVVH5SRANCNFSM54JSUAVQ . You are receiving this because you were mentioned.Message ID: @.***>