MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data

Abstract Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In thi...

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Vydáno v:	Briefings in bioinformatics Ročník 25; číslo 6
Hlavní autoři:	Bosilj, Martin, Suljič, Alen, Zakotnik, Samo, Slunečko, Jan, Kogoj, Rok, Korva, Misa
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Oxford University Press 23.09.2024 Oxford Publishing Limited (England)
Témata:	Bioinformatics Computational Biology - methods COVID-19 - diagnosis COVID-19 - virology Datasets Humans Influenza A Klebsiella Metagenome Metagenomics Metagenomics - methods Pathogens Problem Solving Protocol Rhinovirus SARS-CoV-2 - genetics Severe acute respiratory syndrome coronavirus 2 Software Viral diseases Workflow long reads short PE reads clinical metagenomics pathogen detection bioinformatics workflow
ISSN:	1467-5463, 1477-4054, 1477-4054
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Abstract	Abstract Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets—MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples.
AbstractList	Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets-MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples.Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets-MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples. Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets—MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples. Abstract Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets—MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples.
Author	Slunečko, Jan Korva, Misa Suljič, Alen Bosilj, Martin Kogoj, Rok Zakotnik, Samo
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Cites_doi	10.1101/gr.213959.116 10.3390/genes11080946 10.1186/s13059-019-1891-0 10.3389/fcimb.2022.1021320 10.1038/s41592-022-01431-4 10.1038/s41467-023-41099-8 10.1016/j.cell.2019.07.010 10.12688/f1000research.29032.2 10.5423/PPJ.OA.06.2022.0084 10.1016/j.jmoldx.2021.06.007 10.1007/s13337-012-0075-2 10.3390/v12101164 10.3390/v14112448 10.3390/pathogens10040461 10.1186/s13059-018-1568-0 10.3390/genes10090655 10.1002/rmv.532 10.1016/j.jcv.2021.104908 10.1093/bioinformatics/btz715 10.1128/JCM.01123-18 10.1007/978-981-15-0702-1_1 10.1093/bioinformatics/btab705 10.1038/s41586-020-2012-7 10.1093/bioinformatics/btad293 10.1016/j.jaut.2018.10.005 10.1080/22221751.2020.1725399 10.1371/journal.pone.0218318 10.1016/j.jare.2021.09.012 10.3389/fmicb.2016.00484 10.1016/j.ygeno.2022.110414 10.1101/gr.171934.113 10.1016/j.jcv.2020.104594 10.4161/21597081.2014.979664 10.1186/s40168-017-0317-z 10.1371/journal.pone.0177459 10.1016/j.virol.2017.06.019 10.1111/crj.13538 10.3390/cimb43020061 10.1038/nmeth.1923 10.1093/bioinformatics/btaa490 10.1093/cid/ciy693 10.1016/j.jinf.2019.08.012 10.1186/s13073-021-00991-y 10.1186/s12864-019-6289-6 10.1186/s12859-022-05103-0 10.1093/nar/gkv002 10.3389/fmicb.2015.00224 10.1101/2022.07.07.499093 10.1101/2023.10.20.563221 10.1186/s12859-019-2684-x 10.1101/gr.210641.116 10.3389/fmicb.2017.01069 10.1038/s41592-020-00971-x 10.1093/bioinformatics/btw354 10.1093/bioinformatics/btn322 10.1093/cid/ciaa035 10.1186/s42523-022-00207-7 10.1186/1471-2105-12-385 10.1101/2024.02.19.580813 10.1016/j.jviromet.2013.12.018 10.1038/s41598-019-52881-4 10.1038/s41598-022-13269-z 10.1093/bioinformatics/btp324 10.1016/j.diagmicrobio.2015.06.017 10.3389/fmed.2022.952636 10.1016/j.jcv.2021.104812 10.1038/s41591-020-1105-z 10.1186/s13073-015-0220-9 10.1093/nar/gkab1112 10.1002/imt2.72 10.1038/s41596-022-00738-y 10.1002/cpz1.59 10.1186/gm485 10.3389/fcimb.2023.1224794 10.1371/journal.ppat.1004437 10.1007/978-3-319-78723-7_39 10.1093/gigascience/giab008 10.1186/s12864-022-08985-9 10.1093/cid/cix596 10.1007/s00203-020-02105-5 10.1093/bioinformatics/btv697 10.1186/s12859-024-05634-8 10.1093/bioinformatics/bty149 10.1016/j.diagmicrobio.2019.02.016
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Keywords	long reads short PE reads clinical metagenomics pathogen detection bioinformatics workflow
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References	Sun (2024111623231074900_ref77) 2023; 14 Smith (2024111623231074900_ref63) 2022; 4 Gu (2024111623231074900_ref6) 2021; 27 Bonenfant (2024111623231074900_ref49) 2022 Kim (2024111623231074900_ref83) 2016; 26 Kurtzer (2024111623231074900_ref43) 2017; 12 Carbo (2024111623231074900_ref4) 2020; 131 Mölder (2024111623231074900_ref42) 2021; 10 Wylie (2024111623231074900_ref24) 2018; 56 Naccache (2024111623231074900_ref81) 2014; 24 Miao (2024111623231074900_ref8) 2018; 67 Zhang (2024111623231074900_ref27) 2022; 12 Chrisman (2024111623231074900_ref68) 2022; 12 Wood (2024111623231074900_ref84) 2019; 20 Langmead (2024111623231074900_ref47) 2012; 9 Raju (2024111623231074900_ref16) 2022; 114 Antipov (2024111623231074900_ref80) 2020; 36 Meyer (2024111623231074900_ref59) 2022; 19 Andrews (2024111623231074900_ref44) 2010 Hogan (2024111623231074900_ref79) 2021; 72 Li (2024111623231074900_ref50) 2021; 37 Li (2024111623231074900_ref58) 2009; 25 Chaitanya (2024111623231074900_ref14) 2019 Bidzhieva (2024111623231074900_ref20) 2014; 199 Deng (2024111623231074900_ref82) 2015; 43 Xia (2024111623231074900_ref37) 2023; 2 Lee (2024111623231074900_ref29) 2022; 38 Junier (2024111623231074900_ref31) 2019; 10 Rodríguez-Brazzarola (2024111623231074900_ref38) 2018; 10813 Diao (2024111623231074900_ref10) 2022; 38 Delwart (2024111623231074900_ref17) 2007; 17 Slavov (2024111623231074900_ref19) 2022; 14 Strong (2024111623231074900_ref71) 2014; 10 Sayers (2024111623231074900_ref54) 2022; 50 Zolfo (2024111623231074900_ref85) 2024 Zhou (2024111623231074900_ref5) 2020; 579 Zhang (2024111623231074900_ref9) 2019; 79 Lamprecht (2024111623231074900_ref76) 2019; 97 Hilton (2024111623231074900_ref25) 2016; 7 Mohsin (2024111623231074900_ref15) 2021; 203 Portik (2024111623231074900_ref64) 2022; 23 Morgulis (2024111623231074900_ref55) 2008; 24 Chrzastek (2024111623231074900_ref60) 2017; 509 John (2024111623231074900_ref2) 2021; 43 Kim (2024111623231074900_ref41) 2023; 39 Alawi (2024111623231074900_ref36) 2019; 9 Liang (2024111623231074900_ref72) 2023; 13 2024111623231074900_ref66 Nurk (2024111623231074900_ref53) 2017; 27 Chen (2024111623231074900_ref73) 2022; 16 Marić (2024111623231074900_ref62) 2024; 25 Forbes (2024111623231074900_ref7) 2017; 8 Sangiovanni (2024111623231074900_ref69) 2019; 20 De Coster (2024111623231074900_ref48) 2018; 34 Morsli (2024111623231074900_ref75) 2021; 10 Ye (2024111623231074900_ref1) 2019; 178 Mikheenko (2024111623231074900_ref56) 2016; 32 Chen (2024111623231074900_ref74) 2020; 9 Hall (2024111623231074900_ref21) 2015; 6 Tamames (2024111623231074900_ref39) 2019; 20 Bushnell (2024111623231074900_ref46) 2014 Guo (2024111623231074900_ref13) 2022; 9 Kolmogorov (2024111623231074900_ref57) 2020; 17 Lewandowska (2024111623231074900_ref23) 2017; 5 Breitwieser (2024111623231074900_ref52) 2016 Dutilh (2024111623231074900_ref22) 2014; 4 Breitwieser (2024111623231074900_ref32) Alavandi (2024111623231074900_ref18) 2012; 23 Tran (2024111623231074900_ref65) 2020; 11 Vries (2024111623231074900_ref3) 2021; 138 Greninger (2024111623231074900_ref28) 2015; 7 Lu (2024111623231074900_ref35) 2022; 17 Rosenboom (2024111623231074900_ref67) 2022; 23 Miller (2024111623231074900_ref34) 2013; 5 Moore (2024111623231074900_ref61) 2020; 12 Lewandowska (2024111623231074900_ref86) 2015; 83 Ewels (2024111623231074900_ref45) 2016; 32 Charalampous (2024111623231074900_ref87) 2021; 13 Ramesh (2024111623231074900_ref11) 2019; 14 Ondov (2024111623231074900_ref51) 2011; 12 Ashokan (2024111623231074900_ref70) 2019; 94 Vries (2024111623231074900_ref30) 2021; 141 Somasekar (2024111623231074900_ref26) 2017; 65 Bağcı (2024111623231074900_ref33) 2021; 1 Li (2024111623231074900_ref78) 2023; 13 Zhou (2024111623231074900_ref12) 2021; 23 Danecek (2024111623231074900_ref40) 2021; 10
References_xml	– volume: 27 start-page: 824 year: 2017 ident: 2024111623231074900_ref53 article-title: metaSPAdes: A new versatile metagenomic assembler publication-title: Genome Res doi: 10.1101/gr.213959.116 – volume: 11 start-page: 946 year: 2020 ident: 2024111623231074900_ref65 article-title: Assembling reads improves taxonomic classification of species publication-title: Genes (Basel) doi: 10.3390/genes11080946 – volume: 20 start-page: 257 year: 2019 ident: 2024111623231074900_ref84 article-title: Improved metagenomic analysis with kraken 2 publication-title: Genome Biol doi: 10.1186/s13059-019-1891-0 – volume: 12 start-page: 1021320 year: 2022 ident: 2024111623231074900_ref27 article-title: Clinical value of metagenomic next-generation sequencing by Illumina and nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients publication-title: Front Cell Infect Microbiol doi: 10.3389/fcimb.2022.1021320 – volume: 19 start-page: 429 year: 2022 ident: 2024111623231074900_ref59 article-title: Critical assessment of metagenome interpretation: The second round of challenges publication-title: Nat Methods doi: 10.1038/s41592-022-01431-4 – volume: 14 start-page: 5321 year: 2023 ident: 2024111623231074900_ref77 article-title: Removal of false positives in metagenomics-based taxonomy profiling via targeting type IIB restriction sites publication-title: Nat Commun doi: 10.1038/s41467-023-41099-8 – volume: 178 start-page: 779 year: 2019 ident: 2024111623231074900_ref1 article-title: Benchmarking metagenomics tools for taxonomic classification publication-title: Cell doi: 10.1016/j.cell.2019.07.010 – volume: 10 start-page: 33 year: 2021 ident: 2024111623231074900_ref42 article-title: Sustainable data analysis with Snakemake publication-title: F1000Res doi: 10.12688/f1000research.29032.2 – volume: 38 start-page: 503 year: 2022 ident: 2024111623231074900_ref29 article-title: Nanopore metagenomics sequencing for rapid diagnosis and characterization of lily viruses publication-title: Plant Pathol J doi: 10.5423/PPJ.OA.06.2022.0084 – volume: 23 start-page: 1259 year: 2021 ident: 2024111623231074900_ref12 article-title: Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage in the diagnosis and Management of Pneumonia: A multicenter prospective observational study publication-title: J Mol Diagn doi: 10.1016/j.jmoldx.2021.06.007 – volume: 23 start-page: 88 year: 2012 ident: 2024111623231074900_ref18 article-title: Viral metagenomics: A tool for virus discovery and diversity in aquaculture publication-title: Indian J Virol doi: 10.1007/s13337-012-0075-2 – volume: 12 start-page: 1164 year: 2020 ident: 2024111623231074900_ref61 article-title: Amplicon-based detection and sequencing of SARS-CoV-2 in nasopharyngeal swabs from patients with COVID-19 and identification of deletions in the viral genome that encode proteins involved in interferon antagonism publication-title: Viruses doi: 10.3390/v12101164 – volume: 13 start-page: 1170687 year: 2023 ident: 2024111623231074900_ref78 article-title: The clinical application of metagenomic next-generation sequencing in sepsis of immunocompromised patients. Frontiers in cellular and infection publication-title: Microbiology – volume: 14 start-page: 2448 year: 2022 ident: 2024111623231074900_ref19 article-title: Viral metagenomics for identification of emerging viruses in transfusion medicine publication-title: Viruses doi: 10.3390/v14112448 – volume: 10 start-page: 461 year: 2021 ident: 2024111623231074900_ref75 article-title: Haemophilus influenzae meningitis direct diagnosis by metagenomic next-generation sequencing: A case report publication-title: Pathogens doi: 10.3390/pathogens10040461 – volume-title: KrakenUniq: Confident and Fast Metagenomics Classification Using Unique k-Mer Counts ident: 2024111623231074900_ref32 doi: 10.1186/s13059-018-1568-0 – volume: 10 start-page: 655 year: 2019 ident: 2024111623231074900_ref31 article-title: Viral metagenomics in the clinical realm: Lessons learned from a Swiss-wide ring trial publication-title: Genes doi: 10.3390/genes10090655 – volume: 17 start-page: 115 year: 2007 ident: 2024111623231074900_ref17 article-title: Viral metagenomics publication-title: Rev Med Virol doi: 10.1002/rmv.532 – volume: 141 start-page: 104908 year: 2021 ident: 2024111623231074900_ref30 article-title: Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples publication-title: J Clin Virol doi: 10.1016/j.jcv.2021.104908 – volume-title: Bioinformatics year: 2016 ident: 2024111623231074900_ref52 article-title: Pavian: interactive analysis of metagenomics data for microbiomics and pathogen identification doi: 10.1093/bioinformatics/btz715 – volume: 56 start-page: e01123-18 year: 2018 ident: 2024111623231074900_ref24 article-title: Detection of viruses in clinical samples by use of metagenomic sequencing and targeted sequence capture publication-title: J Clin Microbiol doi: 10.1128/JCM.01123-18 – start-page: 1 volume-title: Structure and Organization of Virus Genomes. Genome and Genomics: From Archaea to Eukaryotes year: 2019 ident: 2024111623231074900_ref14 doi: 10.1007/978-981-15-0702-1_1 – volume: 37 start-page: 4572 year: 2021 ident: 2024111623231074900_ref50 article-title: New strategies to improve minimap2 alignment accuracy publication-title: Bioinformatics doi: 10.1093/bioinformatics/btab705 – volume: 579 start-page: 270 year: 2020 ident: 2024111623231074900_ref5 article-title: A pneumonia outbreak associated with a new coronavirus of probable bat origin publication-title: Nature doi: 10.1038/s41586-020-2012-7 – volume: 39 start-page: btad293 year: 2023 ident: 2024111623231074900_ref41 article-title: VirPipe: An easy-to-use and customizable pipeline for detecting viral genomes from nanopore sequencing publication-title: Bioinformatics doi: 10.1093/bioinformatics/btad293 – volume: 97 start-page: 29 year: 2019 ident: 2024111623231074900_ref76 article-title: Changes in the composition of the upper respiratory tract microbial community in granulomatosis with polyangiitis publication-title: J Autoimmun doi: 10.1016/j.jaut.2018.10.005 – volume: 9 start-page: 313 year: 2020 ident: 2024111623231074900_ref74 article-title: RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak publication-title: Emerging Microbes & Infections doi: 10.1080/22221751.2020.1725399 – volume: 14 start-page: e0218318 year: 2019 ident: 2024111623231074900_ref11 article-title: Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda publication-title: PloS One doi: 10.1371/journal.pone.0218318 – volume: 38 start-page: 201 year: 2022 ident: 2024111623231074900_ref10 article-title: Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections publication-title: Journal of Advanced Research doi: 10.1016/j.jare.2021.09.012 – volume: 7 start-page: 484 year: 2016 ident: 2024111623231074900_ref25 article-title: Metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology publication-title: Front Microbiol doi: 10.3389/fmicb.2016.00484 – volume: 114 start-page: 110414 year: 2022 ident: 2024111623231074900_ref16 article-title: VirusTaxo: Taxonomic classification of viruses from the genome sequence using k-mer enrichment publication-title: Genomics doi: 10.1016/j.ygeno.2022.110414 – volume: 24 start-page: 1180 year: 2014 ident: 2024111623231074900_ref81 article-title: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples publication-title: Genome Res doi: 10.1101/gr.171934.113 – volume: 131 start-page: 104594 year: 2020 ident: 2024111623231074900_ref4 article-title: Coronavirus discovery by metagenomic sequencing: A tool for pandemic preparedness publication-title: J Clin Virol doi: 10.1016/j.jcv.2020.104594 – volume: 4 start-page: e979664 year: 2014 ident: 2024111623231074900_ref22 article-title: Metagenomic ventures into outer sequence space publication-title: Bacteriophage doi: 10.4161/21597081.2014.979664 – volume: 5 start-page: 94 year: 2017 ident: 2024111623231074900_ref23 article-title: Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples publication-title: Microbiome doi: 10.1186/s40168-017-0317-z – volume: 12 start-page: e0177459 year: 2017 ident: 2024111623231074900_ref43 article-title: Singularity: Scientific containers for mobility of compute publication-title: PloS One doi: 10.1371/journal.pone.0177459 – volume: 509 start-page: 159 year: 2017 ident: 2024111623231074900_ref60 article-title: Use of sequence-independent, single-primer-amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses publication-title: Virology doi: 10.1016/j.virol.2017.06.019 – volume: 16 start-page: 646 year: 2022 ident: 2024111623231074900_ref73 article-title: Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases publication-title: Clin Respir J doi: 10.1111/crj.13538 – volume: 43 start-page: 845 year: 2021 ident: 2024111623231074900_ref2 article-title: Next-generation sequencing (NGS) in COVID-19: A tool for SARS-CoV-2 diagnosis, monitoring new strains and phylodynamic modeling in molecular epidemiology publication-title: Curr Issues Mol Biol doi: 10.3390/cimb43020061 – volume: 9 start-page: 357 year: 2012 ident: 2024111623231074900_ref47 article-title: Fast gapped-read alignment with bowtie 2 publication-title: Nat Methods doi: 10.1038/nmeth.1923 – volume: 36 start-page: 4126 year: 2020 ident: 2024111623231074900_ref80 article-title: MetaviralSPAdes: Assembly of viruses from metagenomic data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btaa490 – volume: 67 start-page: S231 year: 2018 ident: 2024111623231074900_ref8 article-title: Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice publication-title: Clin Infect Dis doi: 10.1093/cid/ciy693 – volume: 79 start-page: 419 year: 2019 ident: 2024111623231074900_ref9 article-title: Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults publication-title: J Infect doi: 10.1016/j.jinf.2019.08.012 – volume: 13 start-page: 182 year: 2021 ident: 2024111623231074900_ref87 article-title: Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units publication-title: Genome Med doi: 10.1186/s13073-021-00991-y – volume: 20 start-page: 960 year: 2019 ident: 2024111623231074900_ref39 article-title: Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes publication-title: BMC Genomics doi: 10.1186/s12864-019-6289-6 – volume: 23 start-page: 541 year: 2022 ident: 2024111623231074900_ref64 article-title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets publication-title: BMC Bioinformatics doi: 10.1186/s12859-022-05103-0 – volume: 43 start-page: e46 year: 2015 ident: 2024111623231074900_ref82 article-title: An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkv002 – volume: 6 start-page: 224 year: 2015 ident: 2024111623231074900_ref21 article-title: Beyond research: A primer for considerations on using viral metagenomics in the field and clinic publication-title: Front Microbiol doi: 10.3389/fmicb.2015.00224 – volume-title: Porechop_ABI: Discovering Unknown Adapters in ONT Sequencing Reads for Downstream Trimming year: 2022 ident: 2024111623231074900_ref49 doi: 10.1101/2022.07.07.499093 – ident: 2024111623231074900_ref66 article-title: nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling doi: 10.1101/2023.10.20.563221 – volume-title: BBMap: A Fast, Accurate, Splice-Aware Aligner year: 2014 ident: 2024111623231074900_ref46 – volume: 20 start-page: 168 year: 2019 ident: 2024111623231074900_ref69 article-title: From trash to treasure: Detecting unexpected contamination in unmapped NGS data publication-title: BMC Bioinformatics doi: 10.1186/s12859-019-2684-x – volume: 26 start-page: 1721 year: 2016 ident: 2024111623231074900_ref83 article-title: Centrifuge: Rapid and sensitive classification of metagenomic sequences publication-title: Genome Res doi: 10.1101/gr.210641.116 – volume: 8 start-page: 1069 year: 2017 ident: 2024111623231074900_ref7 article-title: Metagenomics: The next culture-independent game changer publication-title: Front Microbiol doi: 10.3389/fmicb.2017.01069 – volume: 17 start-page: 1103 year: 2020 ident: 2024111623231074900_ref57 article-title: metaFlye: Scalable long-read metagenome assembly using repeat graphs publication-title: Nat Methods doi: 10.1038/s41592-020-00971-x – volume: 32 start-page: 3047 year: 2016 ident: 2024111623231074900_ref45 article-title: MultiQC: Summarize analysis results for multiple tools and samples in a single report publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw354 – volume: 24 start-page: 1757 year: 2008 ident: 2024111623231074900_ref55 article-title: Database indexing for production MegaBLAST searches publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn322 – volume: 72 start-page: 239 year: 2021 ident: 2024111623231074900_ref79 article-title: Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: A multicenter retrospective cohort study publication-title: Clin Infect Dis doi: 10.1093/cid/ciaa035 – volume: 4 start-page: 57 year: 2022 ident: 2024111623231074900_ref63 article-title: Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome publication-title: Animal Microbiome doi: 10.1186/s42523-022-00207-7 – volume-title: FastQC: A Quality Control Tool for High Throughput Sequence Data year: 2010 ident: 2024111623231074900_ref44 – volume: 12 start-page: 385 year: 2011 ident: 2024111623231074900_ref51 article-title: Interactive metagenomic visualization in a web browser publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-385 – year: 2024 ident: 2024111623231074900_ref85 article-title: Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples doi: 10.1101/2024.02.19.580813 – volume: 199 start-page: 68 year: 2014 ident: 2024111623231074900_ref20 article-title: Deep sequencing approach for genetic stability evaluation of influenza a viruses publication-title: J Virol Methods doi: 10.1016/j.jviromet.2013.12.018 – volume: 9 start-page: 16841 year: 2019 ident: 2024111623231074900_ref36 article-title: DAMIAN: An open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples publication-title: Sci Rep doi: 10.1038/s41598-019-52881-4 – volume: 12 start-page: 9863 year: 2022 ident: 2024111623231074900_ref68 article-title: The human “contaminome”: Bacterial, viral, and computational contamination in whole genome sequences from 1000 families publication-title: Sci Rep doi: 10.1038/s41598-022-13269-z – volume: 25 start-page: 1754 year: 2009 ident: 2024111623231074900_ref58 article-title: Fast and accurate short read alignment with burrows-wheeler transform publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 83 start-page: 133 year: 2015 ident: 2024111623231074900_ref86 article-title: Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains publication-title: Diagn Microbiol Infect Dis doi: 10.1016/j.diagmicrobio.2015.06.017 – volume: 9 start-page: 952636 year: 2022 ident: 2024111623231074900_ref13 article-title: Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia publication-title: Front Med doi: 10.3389/fmed.2022.952636 – volume: 138 start-page: 104812 year: 2021 ident: 2024111623231074900_ref3 article-title: Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: Bioinformatic analysis and reporting publication-title: J Clin Virol doi: 10.1016/j.jcv.2021.104812 – volume: 27 start-page: 115 year: 2021 ident: 2024111623231074900_ref6 article-title: Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids publication-title: Nat Med doi: 10.1038/s41591-020-1105-z – volume: 7 start-page: 99 year: 2015 ident: 2024111623231074900_ref28 article-title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis publication-title: Genome Med doi: 10.1186/s13073-015-0220-9 – volume: 50 start-page: D20 year: 2022 ident: 2024111623231074900_ref54 article-title: Database resources of the national center for biotechnology information publication-title: Nucleic Acids Res doi: 10.1093/nar/gkab1112 – volume: 2 start-page: e72 year: 2023 ident: 2024111623231074900_ref37 article-title: Strategies and tools in illumina and nanopore-integrated metagenomic analysis of microbiome data publication-title: iMeta doi: 10.1002/imt2.72 – volume: 17 start-page: 2815 year: 2022 ident: 2024111623231074900_ref35 article-title: Metagenome analysis using the kraken software suite publication-title: Nat Protoc doi: 10.1038/s41596-022-00738-y – volume: 1 start-page: e59 year: 2021 ident: 2024111623231074900_ref33 article-title: DIAMOND+MEGAN: Fast and easy taxonomic and functional analysis of short and long microbiome sequences publication-title: Current Protocols doi: 10.1002/cpz1.59 – volume: 5 start-page: 81 year: 2013 ident: 2024111623231074900_ref34 article-title: Metagenomics for pathogen detection in public health publication-title: Genome Med doi: 10.1186/gm485 – volume: 13 start-page: 1224794 year: 2023 ident: 2024111623231074900_ref72 article-title: Coinfection of SARS-CoV-2 and influenza a (H3N2) detected in bronchoalveolar lavage fluid of a patient with long COVID using metagenomic next−generation sequencing: A case report publication-title: Front Cell Infect Microbiol doi: 10.3389/fcimb.2023.1224794 – volume: 10 start-page: e1004437 year: 2014 ident: 2024111623231074900_ref71 article-title: Microbial contamination in next generation sequencing: Implications for sequence-based analysis of clinical samples publication-title: PLoS Pathog doi: 10.1371/journal.ppat.1004437 – volume: 10813 start-page: 450 year: 2018 ident: 2024111623231074900_ref38 article-title: Analyzing the differences between reads and contigs when performing a taxonomic assignment comparison in metagenomics publication-title: Bioinformatics and Biomedical Engineering doi: 10.1007/978-3-319-78723-7_39 – volume: 10 start-page: giab008 year: 2021 ident: 2024111623231074900_ref40 article-title: Twelve years of SAMtools and BCFtools publication-title: Gigascience doi: 10.1093/gigascience/giab008 – volume: 23 start-page: 748 year: 2022 ident: 2024111623231074900_ref67 article-title: Wochenende—modular and flexible alignment-based shotgun metagenome analysis publication-title: BMC Genomics doi: 10.1186/s12864-022-08985-9 – volume: 65 start-page: 1477 year: 2017 ident: 2024111623231074900_ref26 article-title: Viral surveillance in serum samples from patients with acute liver failure by metagenomic next-generation sequencing publication-title: Clin Infect Dis doi: 10.1093/cid/cix596 – volume: 203 start-page: 865 year: 2021 ident: 2024111623231074900_ref15 article-title: Potential role of viral metagenomics as a surveillance tool for the early detection of emerging novel pathogens publication-title: Arch Microbiol doi: 10.1007/s00203-020-02105-5 – volume: 32 start-page: 1088 year: 2016 ident: 2024111623231074900_ref56 article-title: MetaQUAST: Evaluation of metagenome assemblies publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv697 – volume: 25 start-page: 15 year: 2024 ident: 2024111623231074900_ref62 article-title: Comparative analysis of metagenomic classifiers for long-read sequencing datasets publication-title: BMC Bioinformatics doi: 10.1186/s12859-024-05634-8 – volume: 34 start-page: 2666 year: 2018 ident: 2024111623231074900_ref48 article-title: NanoPack: Visualizing and processing long-read sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty149 – volume: 94 start-page: 331 year: 2019 ident: 2024111623231074900_ref70 article-title: Case report: Identification of intra-laboratory blood culture contamination with Staphylococcus aureus by whole genome sequencing publication-title: Diagn Microbiol Infect Dis doi: 10.1016/j.diagmicrobio.2019.02.016
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Snippet	Abstract Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics... Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the...
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SubjectTerms	Bioinformatics Computational Biology - methods COVID-19 - diagnosis COVID-19 - virology Datasets Humans Influenza A Klebsiella Metagenome Metagenomics Metagenomics - methods Pathogens Problem Solving Protocol Rhinovirus SARS-CoV-2 - genetics Severe acute respiratory syndrome coronavirus 2 Software Viral diseases Workflow
Title	MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data
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