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oushujun
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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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Identify novel LTR sequences
#74
virginiascarlett
closed
4 years ago
1
Does the software work in animal genomes?
#73
zhangleigloria
closed
4 years ago
1
Can LAI be a good metric for contiguous assemblies with a relatively high consensus error rate?
#72
chocotwig
closed
4 years ago
1
LAI is much lower than raw_LAI
#71
bitezhu
closed
4 years ago
6
Are those percentages or decimals for Intact and total LTR in the LAI ouputs
#70
linzhi2013
closed
4 years ago
1
"?" strand direction in 'gff3'
#69
Dobkin-Sun
closed
4 years ago
2
Fix shebang lines and make them more consistent.
#68
jebrosen
closed
4 years ago
1
Intact LTR elements are identified less than expected
#67
oushujun
closed
4 years ago
1
the numbers and bps of all LTRs
#66
Dobkin-Sun
closed
4 years ago
4
Support for non-threaded perl
#65
jebrosen
closed
12 months ago
6
LTR age using local TE library seq
#64
bioteksampath
closed
4 years ago
2
non-redundant LTR library across multiple species
#63
reubwn
closed
4 years ago
3
Update README.md
#62
Juke34
closed
4 years ago
0
Can't locate object method "end" via package "Thread::Queue"
#61
zhangleigloria
closed
4 years ago
2
The total number of LTR in Arabidopsis
#60
wzhjlau2009
closed
4 years ago
8
perl: symbol lookup error
#59
wuxiaopei0509
closed
4 years ago
5
LTR_Retriever RMBlast not installed
#58
RadeshNMP
closed
4 years ago
3
Some errors about :LAI is not applicable on the current genome assembly
#57
123guoxiaoyu
closed
4 years ago
2
Update convert_ltrdetector.pl for new version
#56
baozg
closed
4 years ago
0
Assessing a wheat genome assembly
#55
zhaoruolan
closed
2 months ago
38
Assess animal genome assembly quality using LAI
#54
qiuyixmm
closed
4 years ago
1
Differences between LTR-retriever and RepeatMasker
#53
xiaenhua
closed
4 years ago
1
RepeatMasker: line 28: 25891 Segmentation fault
#52
zhaoruolan
closed
4 years ago
2
too many LTR/unknown and most of LTR/unknown are classified as LTR/Copia
#51
zhangrengang
closed
4 years ago
3
Zombie process is generated when run LTR.identifier.pl
#50
forrwill
closed
4 years ago
2
upload jbrowse with jekyll
#49
CCarine
closed
4 years ago
1
Low LAI for a plant assembly with 100x PacBio data
#48
baozg
closed
4 years ago
7
difference LAI index quick run and full run
#47
KristinaGagalova
closed
4 years ago
2
call_seq_by_list.py error: substr outside of string
#46
lcoombe
closed
5 years ago
5
Problem with The RMblast engine dependency problem
#45
YingHu-jlau
closed
5 years ago
5
Ltr insertion time
#44
mqding0564
closed
5 years ago
26
Dependency checking: The RMblast engine is not installed in RepeatMasker!
#43
Donbbit
closed
5 years ago
13
Length ratio between LTR and the internal region (-max_ratio)
#42
anandksrao
closed
5 years ago
1
soloLTR discovery and reporting
#41
anandksrao
closed
5 years ago
17
call_seq_by_list.pl uninitialized $chr_pre ? It will cause nagative start or end.
#40
YuntaoTan
closed
5 years ago
2
*.pass.list and *.pass.list.gff3 have different row number
#39
SCQUchenyang
closed
5 years ago
2
get flanking regions of all LTRs
#38
reubwn
closed
5 years ago
3
LTR superfamily summary and distribution output
#37
bioteksampath
closed
5 years ago
3
No such file or directory output_by_list.pl line 35
#36
crisvives
closed
5 years ago
2
Can you send me find_ltr_DAWGPAWS.pl you have used?
#35
wangzhennan14
closed
5 years ago
1
invertebrate support
#34
lurebgi
closed
5 years ago
12
Use of uninitialized value $ac/$bd
#33
yuanhelianyi
closed
5 years ago
5
How to solve the ambiguous of whole genome annotation and all LTR-RTs files?
#32
yuanhelianyi
closed
5 years ago
4
What is the meaning of the full, left, right, total, and all in whole-genome LTR-RT annotation files?
#31
yuanhelianyi
closed
5 years ago
3
Best way to get LAI value per contig/scaffold
#30
shkao
closed
5 years ago
2
Questions about *.pass.list
#29
rapaJiahe
closed
5 years ago
2
LTR_retriever reports redundant/duplicated intact LTR-RT from inputs of both LTR_finder and LTR_harvest
#28
b524198065
closed
5 years ago
4
Questions about running LTR_retriever
#27
rapaJiahe
closed
5 years ago
2
Errors in running LTR.identifier.pl
#26
caixu0518
closed
5 years ago
2
INT flag
#25
YuntaoTan
closed
5 years ago
1
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