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The human respiratory tract microbial community structures in healthy and cystic fibrosis infants
Marie-Madlen Pust1,2, Lutz Wiehlmann3, Colin Davenport3, Isa Rudolf1,2, Anna-Maria Dittrich1,2 and Burkhard Tümmler1,2*

1Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Germany
2Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Germany
3Research Core Unit Genomics, Hannover Medical School, Germany

Running title
Airway metagenome of healthy and CF infants

Cite this article
Pust, MM., Wiehlmann, L., Davenport, C. et al. The human respiratory tract microbial community structures in healthy and cystic fibrosis infants. npj Biofilms Microbiomes 6, 61 (2020). https://doi.org/10.1038/s41522-020-00171-7

Reference database
The index of the reference database is available from
https://drive.google.com/open?id=1gl6KiY0gOZiz45ulZaWQCLS6A6Su_hrX.
The multi-FASTA file can also be obtained (see instructions below).

https://sync.academiccloud.de/index.php/s/Zx5YDzT9nnblie4/download

# Unzip the reference database 
gunzip complete_bacterialRefSeqs_201910_2.fasta

# Generate an index of the reference fasta depending on the alignment tool of your choice
samtools faidx complete_bacterialRefSeqs_201910_2.fasta
bwa index complete_bacterialRefSeqs_201910_2.fasta

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R scripts, metadata, input files & reference database

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