From FASTQ to Function: In Silico Methods for Processing Next-Generation Sequencing Data

Mark D Preston; Richard A Stabler

doi:10.1007/978-1-4939-6361-4_3

From FASTQ to Function: In Silico Methods for Processing Next-Generation Sequencing Data

Methods Mol Biol. 2016:1476:23-33. doi: 10.1007/978-1-4939-6361-4_3.

Authors

Mark D Preston¹, Richard A Stabler²

Affiliations

¹ National Institute for Biological Standards and Control, South Mimms, UK.
² Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. [email protected].

PMID: 27507331
DOI: 10.1007/978-1-4939-6361-4_3

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.

Keywords: De novo assembly; Gene annotation; MLST; Read trimming.

MeSH terms

Base Sequence
Clostridioides difficile / classification*
Clostridioides difficile / genetics
Contig Mapping
DNA, Bacterial / analysis*
DNA, Bacterial / genetics
Genome, Bacterial*
High-Throughput Nucleotide Sequencing
Humans
Molecular Sequence Annotation
Multilocus Sequence Typing / methods*
Quality Control
Sequence Analysis, DNA / methods*
Software*

Substances

DNA, Bacterial