Scipediacontent: Scipediacontent moved page Draft Content 708182962 to Bzhalava et al 2017a

2021-02-16T11:21:05Z

Scipediacontent moved page Draft Content 708182962 to Bzhalava et al 2017a

Scipediacontent: Created page with " == Abstract == Motivation Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and c..."

2021-02-16T11:21:01Z

Created page with " == Abstract == Motivation Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and c..."

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== Abstract ==

Motivation Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments. We propose ViraPipe, a scalable metagenome analysis pipeline that is able to analyze thousands of human microbiomes in parallel in tolerable time. The pipeline is tuned for analyzing viral metagenomes and the software is applicable for other metagenomic analyses as well. ViraPipe integrates parallel BWA-MEM read aligner, MegaHit De novo assembler, and BLAST and HMMER3 sequence search tools. We show the scalability of ViraPipe by running experiments on mining virus related genomes from NGS datasets in a distributed Spark computing cluster. Results ViraPipe analyses 768 human samples in 210 minutes on a Spark computing cluster comprising 23 nodes and 1288 cores in total. The speedup of ViraPipe executed on 23 nodes was 11x compared to the sequential analysis pipeline executed on a single node. The whole process includes parallel decompression, read interleaving, BWA-MEM read alignment, filtering and normalizing of non-human reads, De novo contigs assembling, and searching of sequences with BLAST and HMMER3 tools. Contact ilari.maarala@aalto.fi. Availability and implementation https://github.com/NGSeq/ViraPipe.

== Original document ==

The different versions of the original document can be found in:

* [https://academic.oup.com/bioinformatics/article-pdf/34/6/928/25119300/btx702.pdf https://academic.oup.com/bioinformatics/article-pdf/34/6/928/25119300/btx702.pdf]

* [http://academic.oup.com/bioinformatics/article-pdf/34/6/928/25119300/btx702.pdf http://academic.oup.com/bioinformatics/article-pdf/34/6/928/25119300/btx702.pdf],
: [http://dx.doi.org/10.1093/bioinformatics/btx702 http://dx.doi.org/10.1093/bioinformatics/btx702] under the license https://academic.oup.com/journals/pages/about_us/legal/notices

* [http://juuli.fi/Record/0283387617 http://juuli.fi/Record/0283387617],
: [http://dx.doi.org/10.1093/bioinformatics/btx702 http://dx.doi.org/10.1093/bioinformatics/btx702]

* [https://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics34.html#MaaralaBDHB18 https://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics34.html#MaaralaBDHB18],
: [https://academic.oup.com/bioinformatics/article/34/6/928/4587582 https://academic.oup.com/bioinformatics/article/34/6/928/4587582],
: [https://www.ncbi.nlm.nih.gov/pubmed/29106455 https://www.ncbi.nlm.nih.gov/pubmed/29106455],
: [https://doi.org/10.1093/bioinformatics/btx702 https://doi.org/10.1093/bioinformatics/btx702],
: [http://doi.org/10.1093/bioinformatics/btx702 http://doi.org/10.1093/bioinformatics/btx702],
: [https://research.aalto.fi/en/publications/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis-from-next-generation-sequencing-reads(dc2663eb-138f-44e0-9973-dad49b7778d3).html https://research.aalto.fi/en/publications/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis-from-next-generation-sequencing-reads(dc2663eb-138f-44e0-9973-dad49b7778d3).html],
: [https://researchportal.helsinki.fi/fi/publications/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis https://researchportal.helsinki.fi/fi/publications/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis],
: [https://academic.microsoft.com/#/detail/2765816545 https://academic.microsoft.com/#/detail/2765816545]

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Scipediacontent: Scipediacontent moved page Draft Content 708182962 to Bzhalava et al 2017a

Scipediacontent: Created page with " == Abstract == Motivation Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and c..."