nf-rnaSeqMetagen: A nextflow metagenomics pipeline for identifying and characterizing microbial sequences from RNA-seq data

Medicine in Microecology - Tập 4 - Trang 100011 - 2020
Phelelani T. Mpangase1,2, Jacqueline Frost2,3, Michèle Ramsay1,2, Scott Hazelhurst1,4
1Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
2Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
3Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York City, NY, 10029, USA
4School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa

Tài liệu tham khảo

Bakhtiar, 2013, Implications of the human microbiome in inflammatory bowel diseases, FEMS (Fed Eur Microbiol Soc) Microbiol Lett, 342, 10, 10.1111/1574-6968.12111 Martín, 2014, The role of metagenomics in understanding the human microbiome in health and disease, Virulence, 5, 413, 10.4161/viru.27864 Rawat, 2014, MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing, PloS One, 9, 10.1371/journal.pone.0110915 Huttenhower, 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234 Methé, 2012, A framework for human microbiome research, Nature, 486, 215, 10.1038/nature11209 Poretsky, 2014, Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics, PloS One, 9, 10.1371/journal.pone.0093827 Zhang, 2015, Identification of low abundance microbiome in clinical samples using whole genome sequencing, Genome Biol, 16, 265, 10.1186/s13059-015-0821-z Di Tommaso, 2017, Nextflow enables reproducible computational workflows, Nat Biotechnol, 35, 316, 10.1038/nbt.3820 Kurtzer, 2017, Singularity: scientific containers for mobility of compute, PloS One, 12, 10.1371/journal.pone.0177459 Haas, 2013, De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat Protoc, 8, 1494, 10.1038/nprot.2013.084 Trapnell, 2012, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat Protoc, 7, 562, 10.1038/nprot.2012.016 Mele, 2015, The human transcriptome across tissues and individuals, Science, 348, 660, 10.1126/science.aaa0355 Dimon, 2013, IMSA: Integrated Metagenomic Sequence Analysis for identification of exogenous reads in a host genomic background, PloS One, 8, 10.1371/journal.pone.0064546 Visconti, 2018, YAMP: a containerized workflow enabling reproducibility in metagenomics research, GigaScience, 7, 1, 10.1093/gigascience/giy072 Acland, 2014, Database resources of the national center for biotechnology information, Nucleic Acids Res, 42, D7, 10.1093/nar/gkt1146 Wood, 2014, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biol, 15, R46, 10.1186/gb-2014-15-3-r46 Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 Engström, 2013, Systematic evaluation of spliced alignment programs for RNA-seq data, Nat Methods, 10, 1185, 10.1038/nmeth.2722 Conesa, 2016, A survey of best practices for RNA-seq data analysis, Genome Biol, 17, 13, 10.1186/s13059-016-0881-8 Ondov, 2011, Interactive metagenomic visualization in a Web browser, BMC Bioinf, 12, 385, 10.1186/1471-2105-12-385 Lex, 2014, UpSet: visualization of intersecting sets, IEEE Trans Visual Comput Graph, 20, 1983, 10.1109/TVCG.2014.2346248 Frost, 2018, Dysregulation of the Wnt signaling pathway in South African patients with diffuse systemic sclerosis, Clin Rheumatol Katsumoto, 2011, The Pathogenesis of systemic sclerosis, Annu Rev Pathol, 6, 509, 10.1146/annurev-pathol-011110-130312 Fonseca, 2007, A polymorphism in the CTGF promoter region associated with systemic sclerosis, N Engl J Med, 357, 1210, 10.1056/NEJMoa067655 Broen, 2014, The role of genetics and epigenetics in the pathogenesis of systemic sclerosis, Nat Rev Rheumatol, 10, 671, 10.1038/nrrheum.2014.128 Gabrielli, 2009, Scleroderma, N Engl J Med, 360, 1989, 10.1056/NEJMra0806188 Grossman, 2011, Do infections facilitate the emergence of systemic sclerosis?, Autoimmun Rev, 10, 244, 10.1016/j.autrev.2010.09.010 Arron, 2014, High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis, J Invest Dermatol, 134, 2138, 10.1038/jid.2014.127 Murdaca, 2016, Genetic factors and systemic sclerosis, Autoimmun Rev, 15, 427, 10.1016/j.autrev.2016.01.016 Marie, 2015, Environmental risk factors of systemic sclerosis, Semin Immunopathol, 37, 463, 10.1007/s00281-015-0507-3 Radić, 2014, Role of Helicobacter pylori infection in autoimmune systemic rheumatic diseases, World J Gastroenterol, 20, 12839, 10.3748/wjg.v20.i36.12839 Andrews, 2010 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820 Velmurugan, 2017, Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis, Genome Biol, 18, 1, 10.1186/s13059-016-1134-6 Funke, 1998, Characteristics of Arthrobacter cumminsii, the most frequently encountered Arthrobacter species in human clinical specimens, J Clin Microbiol, 36, 1539, 10.1128/JCM.36.6.1539-1543.1998 Wang, 2005, Arthrobacter scleromae sp. nov. isolated from human clinical specimens, J Clin Microbiol, 43, 1451, 10.1128/JCM.43.3.1451-1455.2005 Koerner, 2009, The genus Dietzia: a new home for some known and emerging opportunist pathogens, FEMS Immunol Med Microbiol, 55, 296, 10.1111/j.1574-695X.2008.00513.x Bank, 2016, The role of γδ T Cells in fibrotic diseases, Rambam Maimonides Medical Journal, 7, 10.5041/RMMJ.10256 Tamai, 2018, First case of a bloodstream infection caused by the genus Brachybacterium, J Infect Chemother, 24, 998, 10.1016/j.jiac.2018.06.005 Mages, 2008, Identities of Arthrobacter spp. and Arthrobacter-like bacteria encountered in human clinical specimens, J Clin Microbiol, 46, 2980, 10.1128/JCM.00658-08 Martel, 2008, Devriesea agamarum gen. nov., sp. nov., a novel actinobacterium associated with dermatitis and septicaemia in agamid lizards, Int J Syst Evol Microbiol, 58, 2206, 10.1099/ijs.0.65478-0 Ben Fekih, 2018, Draft genome sequence of Pseudarthrobacter sp. strain AG30, isolated from a gold and copper mine in China, Microbiology Resource Announcements, 7, 4, 10.1128/MRA.01329-18 Tager, 1999, Clinical and laboratory manifestations of systemic sclerosis (scleroderma) in black South Africans, Rheumatology, 38, 397, 10.1093/rheumatology/38.5.397 Cowie, 1990, Features of systemic sclerosis (scleroderma) in South African goldminers, S Afr Med J, 77, 400