TrEMOLO is a bioinformatics tool dedicated to the detection of transposable elements movements using long reads.

This dataverse contains all the data that we used for the TrEMOLO paper: the simulated dataset, the source code of TrEMOLO as well as all the accessory codes.

"TrEMOLO: Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches". Mohamed Mourdas, Sabot François, Varoqui Marion, Mugat Bruno, Audouin Katell, Pélisson Alain, Fiston-Lavier Anna-Sophie, Chambeyron Séverine. bioRxiv 2022.07.21.500944; doi: https://doi.org/10.1101/2022.07.21.500944
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2.3-beta1 version of TrEMOLO
Oct 10, 2023
MOHAMED, Mourdas, 2023, "2.3-beta1 version of TrEMOLO", https://doi.org/10.23708/IEL4HY, DataSuds, V1
New version of TrEMOLO
TrEMOLO-2.3-beta1.zip
Oct 10, 2023 - 2.3-beta1 version of TrEMOLO
ZIP Archive - 61.8 MB - MD5: e03b114cf85c3e7de220b4836f6c6c41
v2.2-beta1 version used for the publication data of TrEMOLO
Dec 19, 2022
SABOT, Francois; MOHAMED, Mourdas, 2022, "v2.2-beta1 version used for the publication data of TrEMOLO", https://doi.org/10.23708/2FYBUL, DataSuds, V2
This dataset is the locked software version used for the publication of TrEMOLO. It represents the v2.2-beta1 version
README-TrEMOLO.md
Dec 19, 2022 - v2.2-beta1 version used for the publication data of TrEMOLO
Markdown Text - 21.3 KB - MD5: 1e7c5b492edcbc27ce15f9432630984a
All the codes used for simulating the genomes and so on
Replication data for simulated reads for S1, S2 and S3 genomes for the TrEMOLO paper
Dec 19, 2022
SABOT, Francois; MOHAMED, Mourdas, 2022, "Replication data for simulated reads for S1, S2 and S3 genomes for the TrEMOLO paper", https://doi.org/10.23708/N447VS, DataSuds, V1
This dataset contains the simulated reads used to validate TrEMOLO. The reads were created using DeeepSimulator v1.5 (https://github.com/liyu95/DeepSimulator/releases/tag/v1.5) using the options -B 2 -K n -l 20000.
TrEMOLO-2.2-beta.zip
Dec 16, 2022 - v2.2-beta1 version used for the publication data of TrEMOLO
ZIP Archive - 45.7 MB - MD5: fbd89eded443d033208d613612c46542
Simulated genome sequences for replication control for TrEMOLO
Dec 16, 2022
SABOT, Francois; MOHAMED, Mourdas, 2022, "Simulated genome sequences for replication control for TrEMOLO", https://doi.org/10.23708/DSDTZ0, DataSuds, V1
This dataset contains the simulated genomes based on the G0-F100 initial sequence including the INSIDERs and OUTSIDERs simulated insertions.
genomesData.tar.gz
Dec 16, 2022 - Simulated genome sequences for replication control for TrEMOLO
Gzip Archive - 115.9 MB - MD5: 7a912bbb0b98eb838c66e7a081e44d0a
Simulated genome sequences for replicating the TrEMOLO benchmarking assays
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