A method for bioinformatic analysis of transposon insertion sequencing (INSeQ) results for identification of microbial fitness determinants

Nengding Wang, Egon Anderson Ozer*

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

Transposon insertion sequencing is a process whereby microbial fitness determinants can be identified on a genome-wide scale. This process uses high-throughput next generation sequencing to screen for changes in the composition of a pool of transposon mutants after exposure to selective conditions. One commonly used process for generating transposon insertion sequencing libraries is called INSeq that works with mutant pools produced using a modified Mariner transposon. Libraries produced using the INSeq process are sequenced on the Illumina platform. In this chapter, we describe our method for processing the raw Illumina sequencing reads, aligning the reads to a reference sequence to determine read counts, and using the online transposon insertion sequencing data analysis server, ESSENTIALS, to interpret the results.

Original languageEnglish (US)
Pages (from-to)243-253
Number of pages11
JournalMethods in Molecular Biology
Volume1498
DOIs
Publication statusPublished - Jan 1 2017

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Keywords

  • Bioinformatics
  • Gene function
  • INSeq
  • Microbial fitness
  • Next-generation sequencing
  • Transposon insertion sequencing

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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