Antibiotics pp E1-E3 | Cite as


  • Peter Sass
Part of the Methods in Molecular Biology book series (MIMB, volume 1520)


Methods and Protocols

In Chapter 20 titled “Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing”, table 3 is incorrect, it is corrected as follows.

Table 3

Software installation procedures (see Note 1)


Commands required for installation


cd ~/methods_protocols/programs; wget; tar xf SPAdes-3.9.0-Linux.tar.gz; cp -r ./SPAdes-3.9.0-Linux/bin/ ./; cp -r ./SPAdes-3.9.0-Linux/share/ ./; rm -rIf SPAdes-3.9.0-Linux.tar.gz SPAdes-3.9.0-Linux/


cd ~/methods_protocols/programs; wget; tar xf ncbi-blast-2.4.0+-x64-linux.tar.gz; cp ./ncbi-blast-2.4.0+/bin/* ./bin/; rm -rIf ncbi-blast-2.4.0+-x64-linux.tar.gz ncbi-blast-2.4.0+/


sudo apt-get install git; cd ~/methods_protocols/programs; git clone; cp ./mlst/bin/* ./bin/; cp -r ./mlst/db/ ./; cp -r ./mlst/perl5/ ./; rm -rIf mlst; sudo cpan Moo List::MoreUtils


sudo apt-get install zlib1g-dev libncurses5-dev; cd ~/methods_protocols/programs; wget; tar xf samtools-1.2.tar.bz2; cd samtools-1.2; make; make prefix=~/methods_protocols/programs install; cd ..; wget; tar xf bcftools-1.2.tar.bz2; cd bcftools-1.2; make; make prefix=~/methods_protocols/programs install; cd ..; rm -rIf samtools-1.2.tar.bz2 samtools-1.2/ bcftools-1.2.tar.bz2 bcftools-1.2/


cd ~/methods_protocols/programs; wget; unzip; cp ./bowtie2-2.2.9/bowtie* ./bin/; rm -rIf bowtie2-2.2.9/


sudo apt-get install g++; cd ~/methods_protocols/programs; wget; tar xf bedtools-2.26.0.tar.gz; cd bedtools2/; make; cd ..; cp ./bedtools2/bin/* ./bin/; rm -rIf bedtools-2.26.0.tar.gz bedtools2/


# Download GATK software from to ~/methods_protocols/programs folder. The following commands are for GATK version 3.6 (they must be adapted to the downloaded version). sudo apt-get install openjdk-8-jdk; cd ~/methods_protocols/programs; tar xf GenomeAnalysisTK-3.6.tar.bz2; chmod +x GenomeAnalysisTK.jar; mv GenomeAnalysisTK.jar ./bin/; rm GenomeAnalysisTK-3.6.tar.bz2


cd ~/methods_protocols/programs; wget; chmod +x picard.jar; mv picard.jar ./bin/

Aspera connect

cd ~/methods_protocols/programs; wget; tar xf aspera-connect-; sh; rm aspera-connect-; cd ~/; cp -Rn .aspera/connect/* ~/methods_protocols/programs/; rm -rIf .aspera/


sudo apt-get install python-dev python-pip; pip install numpy; cd ~/methods_protocols/programs; git clone -b antibiotics_book_chapter; chmod +x ./ReMatCh/; cd bin; ln -s ../ReMatCh/ ./


cd ~/methods_protocols/programs; wget; unzip; rm


sudo apt-get install r-base

Changes have also been made to paragraph 3.2.1 Antibiotic Resistance Databases in the same chapter

§ cd ~/methods_protocols/antibiotic_resistance/
§ wget
§ tar xf broadstreet-v1.1.0.tar.gz
§ mv “nucleotide_fasta[protein homolog model].fasta”
§ rm *
§ mv .nucleotide_fasta_protein_homolog_model.fasta
§ sed --in-place “s# #_#g” nucleotide_fasta_protein_homolog_model.fasta

In Chapter 4 titled “Structure Elucidation of Antibiotics by NMR Spectroscopy”, the running head “Nmr” is replaced by “NMR” and the configuration of the amino acids (Note 53) is updated as “L”. Other author corrections are also updated.

The online version of the original chapter can be found at

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Peter Sass
    • 1
  1. 1.Interfaculty Institute for Microbiology and Infection Medicine, Microbial Bioactive CompoundsUniversity of TübingenTübingenGermany

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