Open AccessProcessing Oxford Nanopore Long Reads Using Amazon Web Services
Author(s) -
Valeriya V. Shapovalova,
Sergey P. Radko,
K. G. Ptitsyn,
George S. Krasnov,
K. V. Nakhod,
O.S Konash,
M.A. Vinogradina,
Elena A. Ponomarenko,
Dmitry S. Druzhilovskiy,
Andrey Lisitsa
Publication year - 2020
Publication title -
biomedical chemistry: research and methods
Language(s) - English
Resource type - Journals
ISSN - 2618-7531
DOI - 10.18097/bmcrm00131
Subject(s) - nanopore sequencing , nanopore , computer science , cloud computing , dna sequencer , computational biology , protocol (science) , transcriptome , dna sequencing , amazon rainforest , dna , data mining , world wide web , biology , genetics , engineering , gene , operating system , medicine , gene expression , alternative medicine , pathology , chemical engineering , ecology
Studies of genomes and transcriptomes are performed using sequencers that read the sequence of nucleotide residues of genomic DNA, RNA, or complementary DNA (cDNA). The analysis consists of an experimental part (obtaining primary data) and bioinformatic processing of primary data. The bioinformatics part is performed with different sets of input parameters. The selection of the optimal values of the parameters, as a rule, requires significant computing power. The article describes a protocol for processing transcriptome data by virtual computers provided by the cloud platform Amazon Web Services (AWS) using the example of the recently emerging technology of long DNA and RNA sequences (Oxford Nanopore Technology). As a result, a virtual machine and instructions for its use have been developed, thus allowing a wide range of molecular biologists to independently process the results obtained using the "Oxford nanopore".