介绍

LTR_retriever（https://github.com/oushujun/LTR_retriever）

工具 | LTR_retriever: 从头识别 LTR - 图1

下载

使用

  1. LTR_retriever -h
  2. ## 
  3. ## ##########################
  4. ## ### LTR_retriever v2.9.0 ###
  5. ## ##########################
  6. ## 
  7. ## A program for accurate identification of LTR-RTs from outputs of LTRharvest and
  8. ##         LTR_FINDER, generates non-redundant LTR-RT library for genome annotations.
  9. ## 
  10. ## Shujun Ou (shujun.ou.1@gmail.com) 03/26/2019
  11. ## 
  12. ## Usage: LTR_retriever -genome genomefile -inharvest LTRharvest_input [options]

输入选项

  1. ## 【Input Options】
  2. ## -genome      [File]     Specify the genome sequence file (FASTA)
  3. ## -inharvest   [File]     LTR-RT candidates from LTRharvest
  4. ## -infinder    [File]     LTR-RT candidates from LTR_FINDER
  5. ## -inmgescan   [File]     LTR-RT candidates from MGEScan_LTR
  6. ## -nonTGCA     [File]     Non-canonical LTR-RT candidates from LTRharvest
  • -genome:
  • -inharvest:
  • -infinder:
  • -inmgescan:
  • -nonTGCA:

输出选项

  1. ## 【Output options】
  2. ## -verbose/-v             Retain intermediate outputs (developer mode)
  3. ## -noanno                 Disable whole genome LTR-RT annotation (no GFF3 output)
  • -verbose/-v:
  • -noanno:

过滤选项

  1. ## 【Filter options】
  2. ## -misschar    [CHR]      Specify the ambiguous character (default N)
  3. ## -Nscreen                Disable filtering ambiguous sequence in candidates
  4. ## -missmax     [INT]      Maximum number of ambiguous bp allowed in a candidate (default 10)
  5. ## -missrate    [0-1]      Maximum percentage of ambiguous bp allowed in a candidate (default 0.8)
  6. ## -minlen      [INT]      Minimum bp of the LTR region (default 100)
  7. ## -max_ratio   [FLOAT]    Maximum length ratio of internal region/LTR region (default 50)
  8. ## -minscore    [INT]      Minimum alignment length (INT/2) to identify tandem repeats (default 1000)
  9. ## -flankmiss   [1-60]     Maximum ambiguous length (bp) allowed in 60bp-flanking sequences (default 25)
  10. ## -flanksim    [0-100]    Minimum percentage of identity for flanking sequence alignment (default 60)
  11. ## -flankaln    [0-1]      Maximum alignment portion allowed for 60bp-flanking sequences (default 0.6)
  12. ## -motif       [[STRING]] Specify non-canonical motifs to search for
  13. ##                         (default -motif [TCCA TGCT TACA TACT TGGA TATA TGTA TGCA])
  14. ## -notrunc                Discard truncated LTR-RTs and nested LTR-RTs (will dampen sensitivity)
  15. ## -procovTE    [0-1]      Maximum portion of allowed for cumulated DNA TE database and LINE database
  16. ##                         lignments (default 0.7)
  17. ## -procovPL    [0-1]      Maximum portion allowed for cumulated plant protein database alignments (default 0.7)
  18. ## -prolensig   [INT]      Minimum alignment length (aa) for LINE/DNA transposase/plant protein alignment (default 30)
  • -misschar
  • -Nscreen
  • -missmax
  • -missrate
  • -minlen
  • -max_ratio
  • -minscore
  • -flankmiss:
  • -flanksim:
  • -flankaln:
  • -motif:
  • -notrunc:
  • -procovTE:
  • -procovPL:
  • -prolensig:

库选项

  1. ## 【Library options】
  2. ## -blastclust  [[STRING]] Trigger to use blastclust and customize parameters
  3. ##                         (default -blastclust [-L .9 -b T -S 80])
  4. ## -cdhit       [[STRING]] Trigger to use cd-hit-est (default) and customize parameters
  5. ##                         (default -cdhit [-c 0.8 -G 0.8 -s 0.9 -aL 0.9 -aS 0.9 -M 0])
  6. ## -linelib     [FASTA]    Provide LINE transposase database for LINE TE exclusion
  7. ##                         (default /database/Tpases020812LINE)
  8. ## -dnalib      [FASTA]    Provide DNA TE transposase database for DNA TE exclusion
  9. ##                         (default /database/Tpases020812DNA)
  10. ## -plantprolib [FASTA]    Provide plant protein database for coding sequence exclusion
  11. ##                         (default /database/alluniRefprexp082813)
  12. ## -TEhmm       [Pfam]     Provide Pfam database for TE identification
  13. ##                         (default /database/TEfam.hmm)
  • -blastclust:
  • -cdhit:
  • -linelib:
  • -dnalib:
  • -plantprolib:
  • -TEhmm:

依赖

  1. ## 【Dependencies】
  2. ## -repeatmasker [path]    Path to the RepeatMasker program. (default: find from ENV)
  3. ## -blastplus   [path]     Path to the BLAST+ program. (default: find from ENV)
  4. ## -blast       [path]     Path to the BLAST program. Required if -blastclust is used. (default: find from ENV)
  5. ## -cdhit_path  [path]     Path to the CD-HIT program. Required if -cdhit is used. (default: find from ENV)
  6. ## -hmmer       [path]     Path to the HMMER program. (default: find from ENV)
  7. ## -trf_path    [path]     Path to the trf program. (default: find from ENV)

设置指定软件的路径，默认从环境变量中获取。

其他

  1. ## 【Miscellaneous】
  2. ## -u           [FLOAT]    Neutral mutation rate (per bp per ya) (default 1.3e-8 (from rice))
  3. ## -step        [STRING]   Restart the program from a particular step. Existing outputs will be overwritten. Options:
  4. ##                                 Init (default, from the beginning);
  5. ##                                 Major (Tandem repeat cleanup finished, structrual analyses next)
  6. ##                                 Trunc (Structural analyses finished, truncated LTR recycle next)
  7. ##                                 Promask (Truncated LTR recycle finished, protein contamination cleanup next)
  8. ##                                 Library (Protein contamination cleanup finished, initial library construction next)
  9. ##                                 Next (Initial library construction finished, non-TGCA analyses next)
  10. ## -threads     [INT]      Number of threads (≤ total available threads, default 4)
  11. ## -help/-h                Display this help information
  • -u:
  • -step:
  • -threads:
  • -help/-h:

运行

  1. convert_ltrdetector.pl
  2. convert_ltr_struc.pl
  3. convert_MGEScan3.0.pl
  1. gt suffixerator \
  2.   -db genome.fa \
  3.   -indexname genome.fa \
  4.   -tis -suf -lcp -des -ssp -sds -dna
  6. gt ltrharvest \
  7.   -index genome.fa \
  8.   -minlenltr 100 \
  9.   -maxlenltr 7000 \
  10.   -mintsd 4 \
  11.   -maxtsd 6 \
  12.   -motif TGCA \
  13.   -motifmis 1 \
  14.   -similar 85 \
  15.   -vic 10 \
  16.   -seed 20 \
  17.   -seqids yes > genome.fa.harvest.scn
  19. LTR_FINDER_parallel \
  20.   -seq genome.fa \
  21.   -threads 10 \
  22.   -harvest_out \
  23.   -size 1000000 \
  24.   -time 300
  26. cat genome.fa.harvest.scn genome.fa.finder.combine.scn > genome.fa.rawLTR.scn
  1. LTR_retriever \
  2.   -genome genome.fa \
  3.   -inharvest genome.fa.rawLTR.scn \
  4.   -threads 10 [options]
  1. LAI \
  2.   -genome genome.fa \
  3.   -intact genome.fa.pass.list \
  4.   -all genome.fa.out [options]

参考

  1. github地址：https://github.com/oushujun/LTR_retriever
  2. xuzhougeng | LTR_retriever: 一个更加准的LTR整合分析工具
  3. Ou S, Jiang N. LTRretriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. _Plant Physiol. 2018 Feb;176(2):1410-1422. doi: 10.1104/pp.17.01310