Table 1 Key resources table

From: Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer

REAGENT or RESOURCE

SOURCE

IDENTIFIER

Biological samples

  

Fecal samples

This study

https://www.Lifelines.nl

Deposited data

LLD baseline metagenomics

European Genome-Phenome Archive (EGA)

EGAD00001001991

LLD follow-up metagenomics

EGA

EGAD00001006959

Software and algorithms

R (version 4.0.3)

R Foundation

https://www.r-project.org/

Python (version 3.7.4)

Python

https://www.python.org

KneadData (version 0.4.6.1)

44

https://huttenhower.sph.harvard.edu/kneaddata/

Megahit

86

https://github.com/voutcn/megahit

dRep (version 3.4.3)

48

https://github.com/MrOlm/drep

Metawrap (version 1.3.2)

46

https://github.com/bxlab/metaWRAP

CheckM (version 1.2.2)

47

https://github.com/Ecogenomics/CheckM

GTDBTk (version 2.1.1)

51

https://github.com/Ecogenomics/GTDBTk

MASH (version 2.3)

49

https://github.com/marbl/Mash

FastANI (version 1.33)

50

https://github.com/ParBLiSS/FastANI

Bowtie 2 (version 2.5.1)

53

https://github.com/BenLangmead/bowtie2

CD-HIT (version 4.8.1)

63

https://sites.google.com/view/cd-hit

Prodigal (version 2.6.3)

64

https://github.com/hyattpd/Prodigal

Barrnap (version 0.9)

87

https://github.com/tseemann/barrnap

Prokka (version 1.14.6)

71

https://github.com/tseemann/prokka

Blastn (version 2.6.0)

58

https://ftp.ncbi.nlm.nih.gov/blast/executables/blast + /LATEST/

eggNOG-mapper (version 2.1.11)

65

http://eggnog5.embl.de

Resistance Gene Identifier (RGI)

67

https://github.com/arpcard/rgi

Traitar (version 1.1.1)

72

https://github.com/hzi-bifo/traitar

Fastspar (version 1.0.0)

25

https://github.com/scwatts/fastspar

UBCGtree (version 2.0)

52

http://leb.snu.ac.kr/ubcg2/about

vegan R package

81

https://cran.r-project.org/web/packages/vegan/index.html

lme4 R package

80

https://cran.r-project.org/web/packages/lme4/index.html

lmtest R package

84

https://cran.r-project.org/web/packages/lmtest/index.html

ggplot2

88

https://cran.r-project.org/web/packages/ggplot2/index.html

igraph v1.2.6

76

https://cran.r-project.org/web/packages/igraph/index.html

ggraph v2.0.5

77

https://cran.r-project.org/web/packages/ggraph/index.html

ncf v 1.3-2

 

https://github.com/objornstad/ncf

lme4qtl v0.2.2

78

https://rdrr.io/github/variani/lme4qtl/man/relmatLmer.html

ComplexHeatmap v2.18.0

89

https://github.com/jokergoo/ComplexHeatmap

Database

Pfam database

66

https://www.ebi.ac.uk/interpro/entry/pfam

dbCAN

90

https://bcb.unl.edu/dbCAN/

CARD database

67

https://card.mcmaster.ca/analyze/rgi

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