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Antibiotics pp E1-E3 | Cite as

Erratum

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

Antibiotics

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)

Name

Commands required for installation

SPAdes

cd ~/methods_protocols/programs; wget http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Linux.tar.gz; 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/

BLAST+

cd ~/methods_protocols/programs; wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.4.0/ncbi-blast-2.4.0+-x64-linux.tar.gz; 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+/

MLST 2

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

Samtools/Bcftools

sudo apt-get install zlib1g-dev libncurses5-dev; cd ~/methods_protocols/programs; wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2; tar xf samtools-1.2.tar.bz2; cd samtools-1.2; make; make prefix=~/methods_protocols/programs install; cd ..; wget https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2; 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/

Bowtie2

cd ~/methods_protocols/programs; wget http://downloads.sourceforge.net/project/bowtiebio/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip; unzip bowtie2-2.2.9-linux-x86_64.zip; cp ./bowtie2-2.2.9/bowtie* ./bin/; rm -rIf bowtie2-2.2.9-linux-x86_64.zip bowtie2-2.2.9/

Bedtools

sudo apt-get install g++; cd ~/methods_protocols/programs; wget https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz; 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/

GATK

# Download GATK software from https://software.broadinstitute.org/gatk/download/ 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

Picard

cd ~/methods_protocols/programs; wget https://github.com/broadinstitute/picard/releases/download/2.6.0/picard.jar; chmod +x picard.jar; mv picard.jar ./bin/

Aspera connect

cd ~/methods_protocols/programs; wget http://download.asperasoft.com/download/sw/connect/3.6.2/aspera-connect-3.6.2.117442-linux-64.tar.gz; tar xf aspera-connect-3.6.2.117442-linux-64.tar.gz; sh aspera-connect-3.6.2.117442-linux-64.sh; rm aspera-connect-3.6.2.117442-linux-64.sh aspera-connect-3.6.2.117442-linux-64.tar.gz; cd ~/; cp -Rn .aspera/connect/* ~/methods_protocols/programs/; rm -rIf .aspera/

ReMatCh

sudo apt-get install python-dev python-pip; pip install numpy; cd ~/methods_protocols/programs; git clone -b antibiotics_book_chapter https://github.com/miguelpmachado/ReMatCh.git; chmod +x ./ReMatCh/rematch.py; cd bin; ln -s ../ReMatCh/rematch.py ./

PHYLOViZ

cd ~/methods_protocols/programs; wget https://bitbucket.org/phyloviz/phyloviz-main/downloads/phyloviz-1.1a.zip; unzip phyloviz-1.1a.zip; rm phyloviz-1.1a.zip

R

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 https://card.mcmaster.ca/download/0/broadstreet-v1.1.0.tar.gz
§ tar xf broadstreet-v1.1.0.tar.gz
§ mv “nucleotide_fasta[protein homolog model].fasta”
.nucleotide_fasta_protein_homolog_model.fasta
§ rm *
§ mv .nucleotide_fasta_protein_homolog_model.fasta
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  http://dx.doi.org/10.1007/978-1-4939-6634-9_4

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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