| Biological Samples |
|
| Faecal samples from a Ethiopian cohort |
This study |
N/A |
| Faecal samples from a Ghanaian cohort |
This study |
N/A |
| Faecal samples from a Tanzanian cohort |
This study |
N/A |
|
| Critical Commercial Assays |
|
| PowerSoil DNA isolation kit |
Qiagen |
Cat No./ID: 12888-100 |
| TruSeq DNA PCR-free Library Prep Kit |
Illumina, California, USA |
20015962 |
| NexteraXT DNA Library Preparation Kit |
Illumina, California, USA |
FC-131-1096 |
|
| Deposited Data |
|
| Raw sequencing data (Ethiopia) |
Pasolli et al., 2019 and this study |
NCBI-SRA BioProject: PRJNA504891 |
| Raw sequencing data (Ghana) |
This study |
NCBI-SRA BioProject: PRJNA529124 |
| Raw sequencing data (Tanzania) |
This study |
NCBI-SRA BioProject: PRJNA529400 |
| All P. copri isolate genomes and MAGs |
This study |
http://segatalab.cibio.unitn.it/data/Pcopri_Tett_et_al.html |
| Raw sequencing data (Ancient metagenomics samples) |
This study |
NCBI-SRA BioProject: PRJEB31971 |
|
| 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 |
| anvi’o (version 2.3.2) |
Eren et al., 2015 |
https://github.com/merenlab/anvio |
| MetaPhlAn2 (version 2.0) |
Truong et al., 2015 |
https://bitbucket.org/biobakery/metaphlan2 |
| Bowtie2 (version 2.2.9) |
Langmead and Salzberg, 2012 |
https://github.com/BenLangmead/bowtie2 |
| blastn (version 2.6.0+) |
Altschul et al., 1990 |
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast |
| CMseq (version dev commit 41082ef) |
|
https://bitbucket.org/CibioCM/cmseq/ |
| Prokka (version 1.11) |
Seemann, 2014 |
https://github.com/tseemann/prokka |
| Pyani (version 0.2.6) |
Pritchard et al., 2015 |
https://github.com/widdowquinn/pyani |
| Roary (version 3.11) |
Page et al., 2015 |
https://github.com/sanger-pathogens/Roary |
| SciPy |
Bressert, 2012 |
https://github.com/scipy/scipy |
| PhyloPhlAn (version dev commit 7c38e19) |
Segata et al., 2013 |
https://bitbucket.org/nsegata/phylophlan |
| Diamond (version v0.9.9.110) |
Buchfink et al., 2015 |
https://github.com/bbuchfink/diamond |
| MAFFT (version v7.310) |
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 |
| FastTree (version 2.1.10) |
Price et al., 2010 |
https://github.com/PavelTorgashov/FastTree |
| RAxML (version 8.1.15) |
Stamatakis, 2014 |
https://github.com/stamatak/standard-RAxML |
| GraPhlAn (version 1.1.3) |
Asnicar et al., 2015 |
https://bitbucket.org/nsegata/graphlan/ |
| EggNOG mapper (version 1.0.3) |
Huerta-Cepas et al., 2017 |
https://github.com/jhcepas/eggnog-mapper |
| HMMSEARCH (version 3.1b2) |
Eddy, 2011 |
https://github.com/guyz/HMM |
| DeDup |
|
https://github.com/apeltzer/DeDup |
| mapDamage2 |
Jónsson et al., 2013 |
https://github.com/ginolhac/mapDamage |
| SAMtools |
Li et al., 2009 |
https://github.com/samtools |
| HaploGrep2 |
Weissensteiner et al., 2016 |
https://github.com/seppinho/haplogrep-cmd |
| PileupCaller |
|
https://github.com/stschiff/sequenceTools/tree/master/src-pileupCaller |
| BEAST (version 2.5.1) |
Bouckaert et al., 2014 |
https://github.com/CompEvol/beast2 |
| Tracer (version 1.7) |
Rambaut et al., 2018 |
https://github.com/beast-dev/tracer/ |
| Schmutzi |
Renaud et al., 2015 |
https://github.com/grenaud/schmutzi |
| ANGSD |
Korneliussen et al., 2014 |
https://github.com/ANGSD/angsd |
| PRANK (version 140603) |
Löytynoja, 2014 |
https://github.com/ariloytynoja/prank-msa |
| Prodigal (version 2.6.3) |
|
https://github.com/hyattpd/Prodigal |
| Barrnap (version 0.9) |
|
https://github.com/tseemann/barrnap |
