|
Chemicals, Peptides, and Recombinant Proteins
|
|
| Man-Rogosa-Sharp (MRS) |
Scharlau Chemie, Barcelona, Spain |
N/A |
|
| Critical Commercial Assays |
|
| PowerSoil DNA Isolation Kit |
MoBio Laboratories Carlsbad, USA |
N/A |
| NexteraXT DNA Library Preparation Kit |
Illumina, California, USA |
N/A |
|
| Deposited Data |
|
| Raw sequencing data |
This paper |
NCBI-SRA BioProject number PRJNA352475 |
| Assembled contigs |
This paper |
https://www.dropbox.com/s/7pygii8khtrriw0/genome_bins.tar.bz2?dl=0 |
|
| Software and Algorithms |
|
| FastqMcf |
Aronesty, 2011 |
https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md |
| BowTie2 |
Langmead and Salzberg, 2012 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| trim_galore |
N/A |
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| MetaPhlAn2 (version 2.6) |
Segata et al., 2012, Truong et al., 2015
|
https://bitbucket.org/biobakery/metaphlan2 |
| Seqtk |
N/A |
https://github.com/lh3/seqtk |
| PanPhlAn |
Scholz et al., 2016 |
https://bitbucket.org/CibioCM/panphlan/wiki/Home |
| StrainPhlAn |
Truong et al., 2017 |
https://bitbucket.org/biobakery/biobakery/wiki/strainphlan |
| RAxML |
Stamatakis, 2014 |
https://sco.h-its.org/exelixis/web/software/raxml/ |
| metaSPAdes (version 3.10.1) |
Nurk et al., 2017 |
http://bioinf.spbau.ru/en/spades3.7 |
| MetaBAT2 (version 2.12.1) |
Kang et al., 2015 |
https://bitbucket.org/berkeleylab/metabat/wiki/Home |
| CheckM (version 1.0.7) |
Parks et al., 2015 |
https://github.com/Ecogenomics/CheckM/wiki |
| BLASTn (version 2.6.0) |
Altschul et al., 1990 |
https://blast.ncbi.nlm.nih.gov |
| pyani (version 0.2.6) |
N/A |
https://github.com/widdowquinn/pyani |
| PhyloPhlAn2 |
Segata et al., 2013 |
https://bitbucket.org/nsegata/phylophlan/wiki/phylophlan2 |
| GraPhlAn |
Asnicar et al., 2015 |
https://bitbucket.org/nsegata/graphlan/wiki/Home |
| Samtools |
Li, 2011, Li et al., 2009
|
http://samtools.sourceforge.net/ |
