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. 2022 Mar 7;15(1):98.
doi: 10.1186/s13104-022-05978-5.

SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments

Nelina Angelova  1 , Theodoros Danis  1   2 , Jacques Lagnel  3 , Costas S Tsigenopoulos  1 , Tereza Manousaki  4
Affiliations

SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments

Nelina Angelova et al. BMC Res Notes. .

Abstract

Objective: The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research.

Results: Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field.

Keywords: Assembly; Container; Genome; Pipeline; de-novo.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The workflow of SnakeCube and its sub-containers. Each box represents the different images available. A and B represent the quality checking steps for short or/and long reads. B and C serve users with only long reads. D combines them all, forming SnakeCube
Fig. 2
Fig. 2
The benchmarking and optimization of SnakeCube based on the L. sceleratus dataset. a Reports of average memory and load monitoring records of three serial runs, with each point representing a rule of the container. b The rules were further independently monitored for their time-scaling efficiency when run multiple times with an increasing thread allowance. The memory properties are reported as in megabytes and only the highest value at any point is recorded. Time is measured in seconds. Rules are presented in the down-right side with their order of appearance
See this image and copyright information in PMC

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