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

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1476)

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.

Key words

Read trimming De novo assembly Gene annotation MLST 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.National Institute for Biological Standards and ControlSouth MimmsUK
  2. 2.Faculty of Infectious & Tropical DiseasesLondon School of Hygiene and Tropical MedicineLondonUK

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