title: From FASTQ to Function: In Silico Methods for Processing Next-Generation Sequencing Data.
abstract: This chapter presents a method to process C. difficile whole-genome next-generation sequencing data straight from the sequencer. Quality control processing and de novo assembly of these data enable downstream analyses such as gene annotation and in silico multi-locus strain-type identification.
authors: National Institute for Biological Standards and Control, South Mimms, UK.
authors: Mark D
authors: MD
authors: Preston
authors: Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. Richard.stabler@lshtm.ac.uk.
authors: Richard A
authors: RA
authors: Stabler
mesh_terms: D001483:Base Sequence; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics; D020451:Contig Mapping; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D058885:Multilocus Sequence Typing / Q000379:methods*; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004269:DNA, Bacterial
keywords: De novo assembly; Gene annotation; MLST; Read trimming