Biological samples |
|
Metagenomic sequences of longitudinal samples |
This paper |
SRA: PRJEB41102 |
|
Deposited data |
|
Gene catalogue nucleotide and amino acid sequences |
This paper |
http://vm-lux.embl.de/∼hildebra/Drama_GC |
Kushugulova et al., 2018 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJEB17632 |
Willmann et al., 2015 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJEB10391 |
Bäckhed et al., 2015 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJEB6456 |
Chu et al., 2017 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA322188 |
Asnicar et al., 2017 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA339914 |
Lee et al., 2017 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA353655 |
Heintz-Buschart et al., 2016 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA289586 |
Human Microbiome Project Consortium, 2012 |
HMP webpage |
N/A |
Kostic et al., 2015 |
https://diabimmune-17.ltdk.helsinki.fi/ |
N/A |
Yassour et al., 2016 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA290381 |
Vatanen et al., 2016 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA290380 |
Ferretti et al., 2018 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA352475 |
Mehta et al., 2018 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA354235 |
Zeevi et al., 2015 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJEB11532 |
Bengtsson-Palme et al., 2015 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJEB7369 |
Raymond et al., 2016 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJEB8094 |
Palleja et al., 2018 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: ERP022986 |
Yassour et al., 2018 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA475246 |
Scholz et al., 2016, Ward et al., 2016
|
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJNA63661 |
Li et al., 2016 |
https://www.ebi.ac.uk/ena/browser/home |
SRA: PRJEB12357 |
|
Software and algorithms |
|
R version 3.6.2 |
R Core Team 2017 |
https://www.r-project.org/ |
Rarefaction scripts |
Saary et al., 2017 |
https://github.com/hildebra/Rarefaction |
Shotgun metagenomic data processing pipeline |
Hildebrand et al., 2019 |
https://github.com/hildebra/MATAFILER |
Read depth windows calculation |
Hildebrand et al., 2019 |
https://github.com/hildebra/rdCover |
Frameshifts fixing in MSAs program |
This paper |
https://github.com/hildebra/MSAfix |
MetaBAT2 version 2.15 |
Kang et al., 2019 |
https://bitbucket.org/berkeleylab/metabat/src/master/ |
sdm version 1.47 |
Hildebrand et al. 2014 |
https://github.com/hildebra/sdm |
MegaHit version 1.2.3 beta |
Li et al. 2015 |
https://github.com/voutcn/megahit |
Prodigal version 2.6.1 |
Hyatt et al., 2010 |
https://github.com/hyattpd/Prodigal |
Bowtie2 version 2.3.4.1 |
Langmead and Salzberg, 2012 |
https://github.com/BenLangmead/bowtie2 |
Samtools version 1.3.1 |
Li et al., 2009 |
http://www.htslib.org/ |
BedTools version 2.21.0 |
Quinlan and Hall, 2010 |
https://github.com/arq5x/bedtools2 |
CD-HIT version 4.6.1 |
Fu et al., 2012 |
http://weizhongli-lab.org/cd-hit/ |
MMseqs2 Version f5a1cdb44c9 96d6be229226b09ecc687646c0c12 |
Steinegger and Söding, 2017 |
https://github.com/soedinglab/MMseqs2 |
CheckM version 1.0.11 |
Parks et al., 2015 |
https://ecogenomics.github.io/CheckM/ |
MAFFT version 7.245 |
Katoh and Standley, 2013 |
https://mafft.cbrc.jp/alignment/software/ |
Trimal version 1.4.rev22 |
Capella-Gutiérrez et al., 2009 |
http://trimal.cgenomics.org/ |
IQ-TREE version 1.6.3a |
Nguyen et al., 2015 |
https://github.com/iqtree/iqtree2 |
iTOL |
Letunic and Bork, 2016 |
https://itol.embl.de/ |
GTDB-TK version 1.3.0 |
Parks et al., 2018 |
https://github.com/Ecogenomics/GTDBTk |
Kraken2 version 2.0.9-beta |
Wood et al., 2019 |
http://ccb.jhu.edu/software/kraken2/ |
Lambda version 1.9.3 |
Hauswedell et al., 2014 |
https://seqan.github.io/lambda/ |
EggNOG-mapper version 2.0.0 |
Huerta-Cepas et al., 2019 |
https://github.com/eggnogdb/eggnog-mapper |
Diamond version 0.9.24.125 |
Buchfink et al., 2015 |
https://github.com/bbuchfink/diamond |
Bcftools mpileup version 1.9 |
Li, 2011 |
https://samtools.github.io/bcftools/howtos/variant-calling.html |
Vegan R package |
Oksanen et al., 2014 |
https://cran.r-project.org/web/packages/vegan/index.html |
FUBAR |
Murrell et al., 2013 |
http://www.hyphy.org/ |
APE |
Paradis et al., 2004 |
https://cran.r-project.org/web/packages/ape/index.html |