Different approaches of metatranscriptome assembly

Anna DRECHSLEROVÁ

Bakalářská práce

Testing of different quality filtering algorithms on contig quality in soil metatranscriptome

Abstract:

This paper was created by analysing 24 samples produced by Next-Generation Sequencing (Illumina). These samples were acquired from different places in Arctic permafrost as a part of MiCryoFun and CRYOvulcan project. The tested data contains forward and reverse sequences which always form pairs for given sample. Four methods were used to evaluate the quality of our samples FASTQC, FLASH, PRINSEQ and TRIMMOMATIC. This test was followed by comparing the work of different assemblers - concretely SPAdes, Megahit and Velvet. The data was then assessed by Quast. As a last step the results were blasted using Diamond and the final organisms classified.

Abstract:

This paper was created by analysing 24 samples produced by Next-Generation Sequencing (Illumina). These samples were acquired from different places in Arctic permafrost as a part of MiCryoFun and CRYOvulcan project. The tested data contains forward and reverse sequences which always form pairs for given sample. Four methods were used to evaluate the quality of our samples FASTQC, FLASH, PRINSEQ and TRIMMOMATIC. This test was followed by comparing the work of different assemblers - concretely SPAdes, Megahit and Velvet. The data was then assessed by Quast. As a last step the results were blasted using Diamond and the final organisms classified.

Keywords

assembly, quality control, metatranscriptome, FASTQC, FLASH, PRINSEQ, TRIMMOMATIC, SPAdes, Megahit, Velvet, Diamond, Quast, filtering, trimming, alignment, Illumina, RNA, permafrost, Arctic, MiCryoFun, CRYOvulcan

Jazyk práce: angličtina

Datum vytvoření / odevzdání či podání práce: 22. 5. 2020

Obhajoba závěrečné práce

• Vedoucí: Ing. Jiří Bárta, Ph.D.

JIHOČESKÁ UNIVERZITA V ČESKÝCH BUDĚJOVICÍCH

Přírodovědecká fakulta

Bakalářský studijní program / obor:
Applied Informatics / Bioinformatics