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Publication
Adaptation of genoqual pipeline to new upstream applications and to run independently from galaxy portal
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Advisor(s)
Abstract(s)
O presente estágio foi realizado no Instituto Gulbenkian de Ciência (IGC) no âmbito do
mestrado em engenharia biológica e química.
O estagiário esteve envolvido com termos e ferramentas usadas em bioinformática,
metagenómica e NGS. A principal tarefa do estagiário focou-se na atualização de uma
pipeline de análises genómicas feito pelo IGC designado por “GenoQual”. O principal
objetivo do estágio do discente focou-se na atualização de uma pipeline de análises
genómicas feito pelo IGC, há vários anos, designado por “GenoQual”. Desde a última
atualização do GenoQual, tem havido uma evolução natural das ferramentas usadas em
bioinformática, surgindo assim novas alternativas e melhorias nas ferramentas usadas pelo
GenoQual. Uma das atualizações mais importantes foi o lançamento do QIIME 2 que trouxe
melhorias e novas funcionalidades em relação ao QIIME ainda em utilização no GenoQual.
A tarefa principal desta dissertação foi a atualização do código Python do pipeline de modo
ser compatível com uma versão mais recente de Python e adicionar novas funcionalidades à
pipeline, nomeadamente a compatibilidade com o QIIME 2 e Kraken2.
O projeto foi organizado em duas etapas distintas, a primeira foi a atualização do código do
GenoQual de Python 2.7 para o novo Python 3.x. A segunda etapa consistiu na atualização
dos softwares utilizados pela versão original do GenoQual de modo garantir que a nova
pipeline era compatível com as novas versões desses softwares para aproveitar as novas
melhorias e funcionalidades provenientes das novas atualizações.
O código do GenoQual foi sucessivamente atualizado de modo ser compatível com o Python
3.8 e foi proposto a adição da nova plataforma de bioinformáticas microbioma QIIME 2 e o
classificador taxonómico Kraken 2 de modo poder realizar analises do tipo 16S e WGS.
The following internship was developed at the Instituto Gulbenkian de Ciência (IGC) in the scope of the master’s biological and chemical engineering degree. The intern dealt with bioinformatics, metagenomics and NGS related terms and tools and focused on the task of updating a pipeline of genomic analyses developed by IGC a few years ago designated as “GenoQual. Ever since GenoQual was last updated, there has been a natural evolution of the tools used in the bioinformatics field, appearing newer alternatives and updates to the tools used by GenoQual. One of the main updates that occurred was the release of QIIME 2 which brought newer upgrades and features in relation to QIIME 1 which GenoQual was still using at the time. The main objective of this internship was to update the Python code used by the pipeline so that it would become compatible with a more recent Python version as well as adding newer functionalities to the GenoQual pipeline, namely the compatibility with QIIME 2 and Kraken 2. The project was organized into two distinct stages; the first was the updating of GenoQual’s Python 2.7 code to the newer Python 3.x version. The second stage was the updating of the packages used by the original version of GenoQual to make sure that the pipeline was still compatible with the newer versions of those required packages, so that it could make use of their improvements and newer functionalities. GenoQual’s code was successively updated to be compatible with Python 3.8 and the addition of the new microbiome bioinformatics QIIME 2 platform and Kraken 2 taxonomic classifier were proposed as additions to the GenoQual pipeline so that it would be able to do both 16S and WGS type analyses.
The following internship was developed at the Instituto Gulbenkian de Ciência (IGC) in the scope of the master’s biological and chemical engineering degree. The intern dealt with bioinformatics, metagenomics and NGS related terms and tools and focused on the task of updating a pipeline of genomic analyses developed by IGC a few years ago designated as “GenoQual. Ever since GenoQual was last updated, there has been a natural evolution of the tools used in the bioinformatics field, appearing newer alternatives and updates to the tools used by GenoQual. One of the main updates that occurred was the release of QIIME 2 which brought newer upgrades and features in relation to QIIME 1 which GenoQual was still using at the time. The main objective of this internship was to update the Python code used by the pipeline so that it would become compatible with a more recent Python version as well as adding newer functionalities to the GenoQual pipeline, namely the compatibility with QIIME 2 and Kraken 2. The project was organized into two distinct stages; the first was the updating of GenoQual’s Python 2.7 code to the newer Python 3.x version. The second stage was the updating of the packages used by the original version of GenoQual to make sure that the pipeline was still compatible with the newer versions of those required packages, so that it could make use of their improvements and newer functionalities. GenoQual’s code was successively updated to be compatible with Python 3.8 and the addition of the new microbiome bioinformatics QIIME 2 platform and Kraken 2 taxonomic classifier were proposed as additions to the GenoQual pipeline so that it would be able to do both 16S and WGS type analyses.
Description
Keywords
Bioinformática Metagenómicas Pipeline Python QIIME 2 NGS Sequenciamento FASTQ Bioinformatics Metagenomics Taxonomy Sequencing