GTO: A toolkit to unify pipelines in genomic and proteomic research

Almeida, João Rafael; Pinho, Armando J.; Oliveira, José Luís; Fajarda, Olga; Pratas, Diogo

doi:10.1016/j.softx.2020.100535

Cited by 12 publications

(11 citation statements)

References 38 publications

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“…TRACESPipe uses 4 approaches to create and maintain its own database. The default approach downloads automatically all viral sequences from the nucleotide NCBI database into a multi-FASTA using GTO [ 22 ] and Entrez [ 23 ] through the accession codes. The second approach downloads NCBI (only) references using the same process.…”

Section: Methodsmentioning

confidence: 99%

“…We use GTO [ 22 ] to identify regions of low complexity [ 30 ]. It includes a DNA compressor that estimates the content along each genome.…”

Section: Methodsmentioning

confidence: 99%

“…Thus, as a control, TRACESPipe estimates the content of exogenous sequences with FALCON-meta [ 11 ] using databases for each respective type. The download and construction of the reference databases are automatically driven by the pipeline using GTO [ 22 ] and Entrez [ 23 ]. The most representative genomes can be aligned according to the reference, for further consensus sequence construction and analysis.…”

Section: Methodsmentioning

confidence: 99%

“…The fragmentation was defined at 200, and the deviation, at 10. The mutation rate, i.e., the simulation of specific SNP percentages, was set with GTO toolkit [ 22 ]. The conditions used are described in Table 2 .…”

Section: Analysesmentioning

confidence: 99%

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A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level

et al. 2020

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Background Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. Findings TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs. Conclusions TRACESPipe’s unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.

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Section: Methodsmentioning

confidence: 99%

“…We use GTO [ 22 ] to identify regions of low complexity [ 30 ]. It includes a DNA compressor that estimates the content along each genome.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Analysesmentioning

confidence: 99%

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A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level

et al. 2020

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“…and the end was fixed to 3. Low-quality data was filtered using a sliding window of 4 with an average quality of 15 and low complexity regions were flagged with GTO (Almeida et al, 2020). Reads shorter than 25 bases were discarded.…”

Section: Virus Analysismentioning

confidence: 99%

The Human Bone Marrow Is Host to the DNAs of Several Viruses

Toppinen

Sajantila

Pratas

et al. 2021

Front. Cell. Infect. Microbiol.

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The long-term impact of viruses residing in the human bone marrow (BM) remains unexplored. However, chronic inflammatory processes driven by single or multiple viruses could significantly alter hematopoiesis and immune function. We performed a systematic analysis of the DNAs of 38 viruses in the BM. We detected, by quantitative PCRs and next-generation sequencing, viral DNA in 88.9% of the samples, up to five viruses in one individual. Included were, among others, several herpesviruses, hepatitis B virus, Merkel cell polyomavirus and, unprecedentedly, human papillomavirus 31. Given the reactivation and/or oncogenic potential of these viruses, their repercussion on hematopoietic and malignant disorders calls for careful examination. Furthermore, the implications of persistent infections on the engraftment, regenerative capacity, and outcomes of bone marrow transplantation deserve in-depth evaluation.

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