Improving SPAdes perfomance

High-efficiency pipeline for EBI metagenomes analysis utilizing SPAdes software
RFBR # 18-54-74004, joint grant with EMBL

Olga Kunyavskaya
Dmitry Antipov
Andrey Prjibelski
Alla Lapidus
Alexander Shlemov
Anton Korobeynikov (Supervisor)

In course of this projects we will adapt metagenomic assembler metaSPAdes for usage in high-efficiency pipeline for metagenomic analysis in EMBL-EBI. Key tasks of this project are: analysis and modification of SPAdes and metaSPAdes algorithms for running on EMBL-EBI computer cluster, determination of computer cluster optimal configuration and parameters of SPAdes and metaSPAdes software in order to achieve most efficient usage of computer cluster resources when running metaSPAdes as a part of pipeline for assembly and analysis of EBI metagenomes, developing of new pipeline for EBI metagenomes assembly, reassembly and analysis of ENA metagenomes and metatranscriptomes. Our work will help to improve pipeline for assembly and analysis of EMBL-EBI metagenomes and to develop new releases of SPAdes metaSPAdes and rnaSPAdes assemblers, effectively using high-performance computer clusters’ resources, which will significantly reduce computational resources demands for genomes, metagenomes and metatranscriptomes assembly.