MTBseq: A comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates

PeerJ

Volumn 2018, Issue 11, 2018, Pages

  Kohl, Thomas Andreas ^a   Utpatel, Christian ^a   Schleusener, Viola ^a   De Filippo, Maria Rosaria ^b   Beckert, Patrick ^a,c   Cirillo, Daniela Maria ^b   Niemann, Stefan ^a,c  

^a RESEARCH CENTER BORSTEL   (Germany)

^b SAN RAFFAELE HOSPITAL   (Italy)

^c German Center for Infection Research   (Germany)

Author keywords

Antibiotic resistance profiling; Automated analysis pipeline; Bacterial epidemiology; Bacterial genome analysis; Mycobacterium tuberculosis complex; Next generation sequencing; Phylogeny; Whole genome sequencing

Indexed keywords

ETHAMBUTOL; ISONIAZID; PYRAZINAMIDE; RIFAMPICIN; STREPTOMYCIN;

ALGORITHM; ANTIBIOTIC RESISTANCE; ARTICLE; BIOINFORMATICS; COMPUTER MODEL; COMPUTER SECURITY; GENE CLUSTER; GENE DELETION; GENE FREQUENCY; GENE INSERTION; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; MYCOBACTERIUM TUBERCULOSIS COMPLEX; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; SANGER SEQUENCING; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE GENOME SEQUENCING;

EID: 85054851920     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.5895     Document Type: Article

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