How best can I find transposons in my genome?

Question

[eennadi]

My objective is to identify transposons within my genome. To achieve this, I am pursuing a specific approach: aligning my genome to a reference and pinpointing regions that are distinct to my genome, subsequently annotating these regions. My initial attempt involved using the Matcher tool, yielding the following results.

Regarding my current approach, I have a couple of questions and considerations:

1. Visualization of Contig Alignments:

I'm seeking a tool that can comprehensively align all the contigs from my genome and present the alignments in a unified view. This would greatly facilitate the analysis process, providing a more consolidated perspective of the alignments.

1. Alternative Methods for Transposon Identification:

In addition to using Matcher, I'm interested in exploring alternative methods for transposon identification within my genome. While RepeatModeler is one option, I'm curious if there are other effective techniques or tools that could complement or enhance my analysis. I'm open to suggestions and insights from the community to optimize my transposon identification workflow. Thank you

########################################
# Program: matcher
# Rundate: Mon 11 Sep 2023 19:01:28
# Commandline: matcher
#    -asequence /data/dnb09/galaxy_db/files/9/5/f/dataset_95f609af-7744-4fc7-99e9-916451e60a47.dat
#    -bsequence /data/dnb09/galaxy_db/files/5/4/d/dataset_54d0ecd0-f68e-47f3-bb29-adf7f57e9e20.dat
#    -outfile /data/jwd05e/main/062/442/62442138/outputs/dataset_8c4e8af1-256e-4cec-8288-9e7813504567.dat
#    -alternatives 1
#    -gapopen 16
#    -gapextend 4
#    -aformat3 markx0
#    -auto
# Align_format: markx0
# Report_file: /data/jwd05e/main/062/442/62442138/outputs/dataset_8c4e8af1-256e-4cec-8288-9e7813504567.dat
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: NODE_1_length_1281197_cov_47.799695
# 2: chr_A
# Matrix: EDNAFULL
# Gap_penalty: 16
# Extend_penalty: 4
#
# Length: 795
# Identity:     494/795 (62.1%)
# Similarity:   494/795 (62.1%)
# Gaps:          42/795 ( 5.3%)
# Score: 1158
# 
#
#=======================================

  375760    375770    375780    375790    375800         
NODE_1 AGCATCAAATGGTATGGTTCCTGTGGAGATAAGATGGGAGCAAGGTGGTG
       ::: :: ::   :::::: :: :: :: ::::  ::: ::::::::::: 
 chr_A AGCTTCTAA---TATGGTCCCAGTCGATATAACCTGGCAGCAAGGTGGTA
   377720       377730    377740    377750    377760     

  375810    375820    375830    375840    375850         
NODE_1 AGAAGGTTTATGTGACAGGGTCCTTCACAAATTGGAGGAAAATGATAGGC
       : :: :: ::::: :: :: :: ::::::  :::::::::::::::::: 
 chr_A ACAAAGTATATGTCACTGGTTCTTTCACAGGTTGGAGGAAAATGATAGGT
      377770    377780    377790    377800    377810     

  375860    375870    375880    375890    375900         
NODE_1 TTAATTCCTGTTGAGTCCGAACCGGGCCATTTCAAGATTAAACTTCAGTT
       ::: : ::  :        ::::        :  :  : ::: : :::::
 chr_A TTAGTACCAATGCCTGATCAACCAAATGTACTGCACGTCAAATTACAGTT
      377820    377830    377840    377850    377860     

  375910    375920    375930    375940    375950         
NODE_1 GGCTCCTGGAACTCATAGATTTAGGTTTATCGTAGACAACCAGCTGAGGT
         :::: :: :: :: :::::::::::::: :: :: ::  :: ::::::
 chr_A ACCTCCAGGTACGCACAGATTTAGGTTTATTGTCGATAATGAGTTGAGGT
      377870    377880    377890    377900    377910     

  375960    375970    375980    375990    376000         
NODE_1 TTAGTGATAACTTACCTACTGCAACTGATCAAATGGGTAATTTTGTTAAT
       ::::::::  : : :: :: :: :: :: ::::::::::: ::::: :: 
 chr_A TTAGTGATTTCCTTCCAACGGCTACAGACCAAATGGGTAACTTTGTCAAC
      377920    377930    377940    377950    377960     

  376010    376020    376030    376040    376050         
NODE_1 TATTTGGAGGTCTCGGCGGTTCCGAAGTCAGACTCCACGTCATCAAGAAC
       ::: ::::: :  :: : ::: :             : ::  : : ::: 
 chr_A TATCTGGAGATTGCGCCCGTTGC-------------AGGTACTGATGAAA
      377970    377980                 377990    378000  

  376060    376070    376080    376090    376100         
NODE_1 AGGTAAGGAAAGGAAAGATAAAAATAAGAAATCTGTGAGTAAAGT-ATCG
       :   :     :  ::    : :: :   :     :: ::: : :: ::  
 chr_A AACCACCTCCATTAACCCCACAAGTGTCAG----GTAAGTCAGGTGATGA
         378010    378020    378030        378040        

   376110     376120    376130    376140    376150       
NODE_1 AAGGATAG-GTCTACCGTGGGACCATTAAGTGCTAGGTCCTGTATAGCGT
       ::::: :: : :::            : :::::::: ::  : :: ::: 
 chr_A AAGGAAAGAGCCTA------------TGAGTGCTAGATCAAGGATTGCGC
   378050    378060                378070    378080      

    376160    376170    376180    376190    376200       
NODE_1 TAGAAATAGAAAAAGAGCCTGATGATTTTGGAGATGGGTACACCAGATAT
       : :::::::::: ::: :: :::::::: ::  ::::::: :   : :  
 chr_A TTGAAATAGAAAGAGAACCAGATGATTTAGGTAATGGGTATAGTCGTTTC
     378090    378100    378110    378120    378130      

    376210     376220    376230    376240    376250      
NODE_1 CATGAAGAACTC-CCACAAGAACCAAAATACGAATTTAGTTCAGAGATCC
       :::::  : ::: ::::  ::  :::: :: :::: :: :   :: :: :
 chr_A CATGAT-ACCTCGCCACTGGAGACAAAGTATGAATATACTCAGGATATTC
     378140     378150    378160    378170    378180     

     376260    376270    376280    376290          376300
NODE_1 CTGCTATATTTGTAGATCAGTCCATAATCGAGCAGT------TAACAATG
       ::::: : ::    ::::      : :: :::::::      : ::  : 
 chr_A CTGCTGTCTTCACGGATCCTAATGTCATGGAGCAGTACTACCTGACTCTA
      378190    378200    378210    378220    378230     

           376310    376320    376330    376340    376350
NODE_1 GAAAGGCAAAGAAAGAAATCCAATAATATGGCATGGTTGACACCGCCTCA
       ::    ::::  :: ::   : : :: ::::: ::: : :: :: :: ::
 chr_A GATCAACAAAAGAACAACCACCAAAACATGGCCTGGCTAACTCCACCACA
      378240    378250    378260    378270    378280     

           376360    376370    376380    376390    376400
NODE_1 GTTACCACCACAATTAGAAAACGTAATACTTAATAAATTCGGAGAGCCAT
       :::::: :::::  : :: :: :: :: :: ::::  : :    :  :  
 chr_A GTTACCCCCACATCTCGAGAATGTTATTCTGAATAGCTACTCTAATGCGC
      378290    378300    378310    378320    378330     

           376410    376420    376430    376440    376450
NODE_1 TGAGTCAAAGCACGGAGAACAATGCAGGTGCGCTACCAATCCCTAATCAT
          :: ::   :  :: :: ::  :::::::  : :: :: :: ::::::
 chr_A AAGGTGAATCTAACGAAAATAACTCAGGTGCTTTGCCTATACCAAATCAT
      378340    378350    378360    378370    378380     

           376460    376470    376480    376490    376500
NODE_1 TCTGTGTTAAACCATCTGGTAACAACAAGCATTAAACACAACACACTCTG
           : ::::: ::: : :  :: :  :: ::::: :::::::: :: ::
 chr_A GTGATATTAAATCATTTAGCCACCAGTAGTATTAAGCACAACACTCTTTG
      378390    378400    378410    378420    378430     

           376510    376520    376530    376540     
NODE_1 TGTTGCAACAAACAACAGGTACAGGCAGAAGTACGTCTCACAGAT
       ::::::  : :     ::::: :     :: :: ::  :::: ::
 chr_A TGTTGCTTCGATTGTTAGGTATAAAAGAAAATATGTTACACAAAT
      378440    378450    378460    378470    378480


#---------------------------------------
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Answer 1

[Philipp Bayer]

1) It really depends on how many contigs you have; if it's thousands, then any visualisation tool will croak. For a few dozen to hundreds I've had some success with loading minimap2's alignment paf files into pafr: https://github.com/dwinter/pafr

2) I'd just run your assembly through EDTA, which combines several de novo TE annotation tools and gives you a consensus TE library https://github.com/oushujun/EDTA

[eennadi]

Thanks Philipp, I ran my assembly through EDTA, it ended with annotation inconsistency.

[Philipp Bayer]

I've had some success in re-evaluating class annotations from EDTA using TEsorter (https://github.com/zhangrengang/TEsorter), or is it a different issue? I'm not sure what inconsistency you mean here