Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification

Breitwieser, Florian P.; Salzberg, Steven L.

doi:10.1101/084715

Cited by 63 publications

(56 citation statements)

References 16 publications

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“…The assembly was done with SPAdes v.3.6.0 option -meta (19). The alignments were visualized using Pavian (20). All available human hepegivirus-1 genome sequences were compared in SeaView (21); the multiple sequence analysis was done with Clustal Omega (22), and phylogeny reconstruction was done for NS5B sequences in MEGA7 using the Jukes-Cantor model and maximum likelihood algorithm with 1000 bootstrap replicates used to calculate branch strength(23).…”

Section: Methodsmentioning

confidence: 99%

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs

et al. 2017

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Background Next-generation metagenomic sequencing (NGMS) has opened new frontiers in microbial discovery but has been clinically characterized in only a few settings. Objective To explore the plasma virome of persons who inject drugs while characterizing the sensitivity and accuracy of NGMS compared to quantitative clinical standards. Design Longitudinal and cross-sectional studies. Participants Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) co-infected persons enrolled in a clinical trial (NCT01285050) and/or a well-characterized cohort study of persons who have injected drugs. Measurements Viral nucleic acid in plasma by NGMS and quantitative polymerase chain reaction (PCR). Results NGMS generated a total of 600 million reads, which included the expected HIV and HCV RNA sequences. HIV and HCV reads were consistently identified only when samples contained >10,000 copies or IU/ml as determined by quantitative PCR. A novel RNA virus, human hepegivirus-1 (HHpgV-1) was also detected by NGMS in 4 samples from 2 persons in the clinical trial. Because of this unexpected finding, using a quantitative PCR assay for HHpgV-1, infection was also detected in 17 (10.9%) of 156 members of a cohort of persons who injected drugs in whom HHpgV-1 viremia persisted for a median of at least 4538 days and was associated with detection of other bloodborne viruses such as HCV RNA and SEN virus D Limitations The medical importance of HHpgV-1infection remains unknown. Conclusions Although NGMS is insensitive to detection of viruses with relatively low plasma nucleic acid concentrations, it may have a broad potential for discovery of new viral infections of potential medical importance like HHpgV-1.

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Section: Methodsmentioning

confidence: 99%

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs

et al. 2017

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“…Sunbeam's extension framework promotes reproducible analyses and greatly simplifies performing the same type of analysis on multiple datasets. Extension templates, as well as a number of pre-built extensions for metagenomic analysis and visualization software like Anvi'o [51], MetaPhlAn [49], and Pavian [55], are available on our GitHub page (https://github.com/sunbeam-labs).…”

Section: Resultsmentioning

confidence: 99%

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

Clarke

Taylor

Zhao

et al. 2018

Preprint

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“…We performed a taxonomic assignment of reads in each sample using the Centrifuge metagenome classifier Version 1.0.3 together with its associated p+h+v database [43]. Centrifuge reports were converted to Kraken-style reports using Centrifuge’s kreport parameter and Pavian was used to visualize the reports [44]. Taxa with a relative abundance of <5% were discarded as potential kit contaminants and we then evaluated the reports for the presence of potential pathogens and endosymbionts.…”

Section: Methodsmentioning

confidence: 99%

Metagenomic profiling of ticks: identification of novel rickettsial genomes and detection of tick borne canine parvovirus

Ray

Ereqat²,

Al-Jawabreh

et al. 2018

Preprint

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48recovering genome sequences from an unexpected pathogen (canine parvovirus) 49 and a previously unsequenced pathogen (Candidatus Rickettsia barbariae), we50 demonstrate the open-ended nature of metagenomics. We also provide evidence Page 3 of 31 51 that ticks can carry canine parvovirus, raising the possibility that ticks might 52 contribute to the spread of this troublesome virus. 53 Author Summary 54 We have shown how DNA sequencing can be used to detect and characterise 55 potentially pathogenic microorganisms carried by ticks. We surveyed hard ticks 56 collected from domesticated animals across the West Bank territory of Palestine. All 57 the ticks came from species that are also capable of feeding on humans. We 58 detected several important pathogens, including two species of Rickettsia, the sheep 59 pathogen Anaplasma ovis and canine parvovirus. These findings highlight the 60 importance of hard ticks and the hazards they present for human and animal health 61 in Palestine and the opportunities presented by high-throughput sequencing and 62 bioinformatics analyses of DNA sequences in this setting. 63 64

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Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification

Cited by 63 publications

References 16 publications

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

Metagenomic profiling of ticks: identification of novel rickettsial genomes and detection of tick borne canine parvovirus

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