Transposition event detection tool deTEct using NGS alignment data and SV calling outputs (VCF files) from PBSV or Sniffles. deTEct is part of TransposonUltimate.
- Input: Structural variants (VCF file) of PBSV (on PBMM2 alignments) or Sniffles (on NGMLR alignments), transposon annotations (by resonaTE), reference genome (FASTA)
- Output: Annotation and classification of detected transposition events (GFF3).
Installation as CondaPackage:
conda install -c derkevinriehl transposition_detector_detect
Note: Otherwise you can find all source codes in this Github repository.
(using demo files of this repository, we use reference genome CB4856 and probe alignments SX3351)
transposition_deTEct -help
# demo for sniffles_ngmlr alignments
transposition_deTEct -seqHeadTXT demoFiles/sequence_heads.txt -transpGFF3 demoFiles/FinalAnnotations_Transposons.gff3 -assmFasta demoFiles/sequence_CB4856.fasta -svTool sniffles -svFile demoFiles/SX3351_addisababa.sniffles_ngmlr.vcf -outParsedFile demoFiles/sniffles_ngmlr/SX3351_addisababa.SV.vcf.gff3 -outResultFile demoFiles/sniffles_ngmlr/SX3351_addisababa.transpositionEvents.gff3
# demo for pbsv_pbsmm2 alignments
transposition_deTEct -seqHeadTXT demoFiles/sequence_heads.txt -transpGFF3 demoFiles/FinalAnnotations_Transposons.gff3 -assmFasta demoFiles/sequence_CB4856.fasta -svTool pbsv -svFile demoFiles/SX3351_addisababa.pbsv_pbmm2.vcf -outParsedFile demoFiles/pbsv_pbmm2/SX3351_addisababa.SV.vcf.gff3 -outResultFile demoFiles/pbsv_pbmm2/SX3351_addisababa.transpositionEvents.gff3
| Parameter | Mandatory | Description |
|---|---|---|
| seqHeadTXT | (mandatory) | Sequence head names, TXT file (produced by reasonaTE) |
| transpGFF3 | (mandatory) | Transposon annotation file, GFF3 file (produced by reasonaTE) |
| assmFasta | (mandatory) | Assembly file of reference genome, FASTA file |
| svTool | (mandatory) | Structural variant detection tool: "pbsv" or "sniffles" |
| svFile | (mandatory) | Structural variant detection output file, VCF file |
| outParsedFile | (mandatory) | Target file for VCF parsed outputs |
| outResultFile | (mandatory) | Target file for final results with transposition events |
SX3351_addisababa.SV.vcf.gff3.matches.gff3
For each filtered structural variant a set of potential transposon annotation candidates (IDs similar to transposon annotation file) is reported:
seq1 PBSV duplication 2909118 2910241 . + . ['23769', '23770', '23771'];Sseq1TYPE=DUP;END=2910240;Sseq1LEN=1122
seq1 PBSV deletion 163800 164962 . + . ['1', '11827 '];Sseq1TYPE=DEL;END=164961;Sseq1LEN=-1161
seq1 PBSV deletion 290360 290514 . + . ['11843 '];Sseq1TYPE=DEL;END=290513;Sseq1LEN=-153
seq1 PBSV insertion 343890 344420 . + . ['538 '];merged;Sseq1TYPE=seq4NS;END=344424;Sseq1LEN=533
...
SX3351_addisababa.transpositionEvents.gff3
For each final structural variant that is considered to be a transposition event, the given transposon annotation (IDs similar to transposon annotation file) and predicted class are reported:
seq1 PBSV deletion 290360 290514 . + . Transposon=11843;Class=2/1/2(hAT,TIR,DNATransposon);Sseq1TYPE=DEL;END=290513;Sseq1LEN=-153
seq1 PBSV insertion 610241 614786 . + . Transposon=545;Class=2/1/3(CMC,TIR,DNATransposon);merged;merged;Sseq1TYPE=seq4NS;END=611763;Sseq1LEN=1521
seq1 PBSV deletion 879772 884345 . + . Transposon=556;Class=1/1/2(Gypsy,LTR,Retrotransposon);Sseq1TYPE=DEL;END=884344;Sseq1LEN=-4572
seq1 PBSV insertion 1126531 1126860 . + . Transposon=23592;Class=2/1/1(Tc1-Mariner,TIR,DNATransposon);Sseq1TYPE=seq4NS;END=1126859;Sseq1LEN=327
...
Please cite our paper if you find TransposonUltimate useful:
Kevin Riehl, Cristian Riccio, Eric A Miska, Martin Hemberg, TransposonUltimate: software for transposon classification, annotation and detection, Nucleic Acids Research, 2022; gkac136, https://doi.org/10.1093/nar/gkac136
@article{riehl2022transposonultimate,
title={TransposonUltimate: software for transposon classification, annotation and detection},
author={Riehl, Kevin and Riccio, Cristian and Miska, Eric and Hemberg, Martin},
journal={Nucleic Acids Research},
year={2022}
}
We would like to thank Sarah Buddle, Simone Procaccia, Fu Xiang Quah and Alexandra Dallaire for their assistance with testing and debugging the software.