| Biological Samples |
|
| Stool samples from Madagascar cohort |
Golden et al., 2017 |
N/A |
| Stool samples from Ethiopian cohort |
This paper |
N/A |
|
| Critical Commercial Assays |
|
| PowerSoil DNA Isolation Kit |
MoBio Laboratories Carlsbad, USA |
Catalog No. 12888-50 |
| NexteraXT DNA Library Preparation Kit |
Illumina, California, USA |
FC-131-1096 |
|
| Deposited Data |
|
| Raw sequencing data (Madagascar cohort) |
This paper |
NCBI-SRA BioProject: PRJNA485056 |
| Raw sequencing data (Ethiopian cohort) |
This paper |
NCBI-SRA BioProject: PRJNA504891 |
| Data for all genomes |
This paper |
http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html |
| Representative genome for Ca. Cibiobacter qucibialis |
This paper |
DDBJ/ENA/GenBank accession SAUS00000000
|
|
| Software and Algorithms |
|
| metaSPAdes (version 3.10.1) |
Nurk et al., 2017 |
https://github.com/ablab/spades/releases |
| MEGAHIT (version 1.1.1) |
Li et al., 2015 |
https://github.com/voutcn/megahit |
| MetaBAT2 (version 2.12.1) |
Kang et al., 2015 |
https://bitbucket.org/berkeleylab/metabat |
| CheckM (version 1.0.7) |
Parks et al., 2015 |
https://github.com/Ecogenomics/CheckM |
| CMSeq (version 1.0.0) |
This study |
https://bitbucket.org/CibioCM/cmseq |
| Mash (version 2.0) |
Ondov et al., 2016 |
https://github.com/marbl/Mash |
| MetaPhlAn2 (version 2.0) |
Segata et al., 2012b, Truong et al., 2015
|
https://bitbucket.org/biobakery/metaphlan2 |
| HUMANn2 (version 0.7.1) |
Franzosa et al., 2018 |
https://bitbucket.org/biobakery/humann2/ |
| Bowtie2 (version 2.2.9) |
Langmead and Salzberg, 2012 |
https://github.com/BenLangmead/bowtie2 |
| Prodigal (version 2.6.3) |
|
https://github.com/hyattpd/Prodigal |
| Pyani (version 0.2.6) |
Pritchard et al., 2016 |
https://github.com/widdowquinn/pyani |
| StrainPhlAn (version 2.0.0) |
Truong et al., 2017 |
https://bitbucket.org/biobakery/metaphlan2 |
| Anvi’o (version 4) |
Eren et al., 2015 |
https://github.com/merenlab/anvio |
| BWA (version 0.7.17) |
Li and Durbin, 2009 |
https://github.com/lh3/bwa |
| CONCOCT (version 0.5.0) |
Alneberg et al., 2014 |
https://github.com/BinPro/CONCOCT |
| RPSBlast |
Marchler-Bauer et al., 2003 |
ftp://ftp.ncbi.nih.gov/blast/executables/ |
| PhyloPhlAn (version dev, 0.25) |
Segata et al., 2013 |
https://bitbucket.org/nsegata/phylophlan |
| Diamond (version 0.9.9.110) |
Buchfink et al., 2015 |
https://github.com/bbuchfink/diamond |
| mafft (version 7.310) |
Katoh and Standley, 2013 |
https://github.com/The-Bioinformatics-Group/Albiorix/wiki/mafft |
| trimal (version 1.2rev59) |
Capella-Gutiérrez et al., 2009 |
https://github.com/scapella/trimal |
| RAxML (version 8.1.15) |
Stamatakis, 2014 |
https://github.com/stamatak/standard-RAxML |
| IQ-TREE (version 1.6.6) |
Nguyen et al., 2015 |
https://github.com/Cibiv/IQ-TREE |
| Roary (version 3.8) |
Page et al., 2015 |
https://github.com/sanger-pathogens/Roary |
| blastn (version 2.6.0+) |
Altschul et al., 1990 |
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast |
| FastTree (version 2.1.9) |
Price et al., 2010 |
https://github.com/PavelTorgashov/FastTree |
| ecodist R package |
Goslee and Urban, 2007 |
https://github.com/cran/ecodist |
| GraPhlAn (version 1.1.3) |
Asnicar et al., 2015 |
https://bitbucket.org/nsegata/graphlan/ |
| FigTree (version 1.4.3) |
N/A |
http://tree.bio.ed.ac.uk/software/figtree/ |
| Prokka (version 1.12) |
Seemann, 2014 |
https://github.com/tseemann/prokka |
| EggNOG mapper (version 1.0.3) |
Huerta-Cepas et al., 2017 |
https://github.com/jhcepas/eggnog-mapper |
| HMM |
Eddy, 2011 |
https://github.com/guyz/HMM |
| Barrnap (version 0.9) |
N/A |
https://github.com/tseemann/barrnap |
| RDP (version 2.11) |
Cole et al., 2014, Wang et al., 2007
|
https://github.com/rdpstaff/classifier |
|
| Other |
|
| curatedMetagenomicData |
Pasolli et al., 2017 |
https://github.com/waldronlab/curatedMetagenomicData |
| UniProt |
The UniProt Consortium, 2017 |
https://github.com/ebi-uniprot |
| NCBI GenBank database |
NCBI Resource Coordinators, 2013 |
https://www.ncbi.nlm.nih.gov/genbank/ |
| RefSeq (viral genomes and plasmids) |
Brister et al., 2015, O’Leary et al., 2016
|
https://www.ncbi.nlm.nih.gov/refseq/ |
