Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Abstract Background Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, m...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-03-01
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| Series: | Microbiome |
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| Online Access: | http://link.springer.com/article/10.1186/s40168-019-0658-x |
| _version_ | 1828404346659799040 |
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| author | Erik L. Clarke Louis J. Taylor Chunyu Zhao Andrew Connell Jung-Jin Lee Bryton Fett Frederic D. Bushman Kyle Bittinger |
| author_facet | Erik L. Clarke Louis J. Taylor Chunyu Zhao Andrew Connell Jung-Jin Lee Bryton Fett Frederic D. Bushman Kyle Bittinger |
| author_sort | Erik L. Clarke |
| collection | DOAJ |
| description | Abstract Background Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes. Results We present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. A unique component of the Sunbeam pipeline is an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated. Conclusions Sunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic, low-complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3. |
| first_indexed | 2024-12-10T10:34:46Z |
| format | Article |
| id | doaj.art-56cc1c964e0d4947b4e19e5831d07f81 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-10T10:34:46Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-56cc1c964e0d4947b4e19e5831d07f812022-12-22T01:52:27ZengBMCMicrobiome2049-26182019-03-017111310.1186/s40168-019-0658-xSunbeam: an extensible pipeline for analyzing metagenomic sequencing experimentsErik L. Clarke0Louis J. Taylor1Chunyu Zhao2Andrew Connell3Jung-Jin Lee4Bryton Fett5Frederic D. Bushman6Kyle Bittinger7Department of Microbiology, University of PennsylvaniaDepartment of Microbiology, University of PennsylvaniaDivision of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of PhiladelphiaDepartment of Microbiology, University of PennsylvaniaDivision of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of PhiladelphiaDivision of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of PhiladelphiaDepartment of Microbiology, University of PennsylvaniaDivision of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of PhiladelphiaAbstract Background Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes. Results We present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. A unique component of the Sunbeam pipeline is an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated. Conclusions Sunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic, low-complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.http://link.springer.com/article/10.1186/s40168-019-0658-xSunbeamShotgun metagenomic sequencingSoftwarePipelineQuality control |
| spellingShingle | Erik L. Clarke Louis J. Taylor Chunyu Zhao Andrew Connell Jung-Jin Lee Bryton Fett Frederic D. Bushman Kyle Bittinger Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments Microbiome Sunbeam Shotgun metagenomic sequencing Software Pipeline Quality control |
| title | Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments |
| title_full | Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments |
| title_fullStr | Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments |
| title_full_unstemmed | Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments |
| title_short | Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments |
| title_sort | sunbeam an extensible pipeline for analyzing metagenomic sequencing experiments |
| topic | Sunbeam Shotgun metagenomic sequencing Software Pipeline Quality control |
| url | http://link.springer.com/article/10.1186/s40168-019-0658-x |
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