Datasets for Lupo et al. (2022) An extended reservoir of class-D beta-lactamases in non-clinical bacterial strains

Lupo et al. 2022: Archive content for v2Overview...

17 directories, 182 files
README.md: this file.command-line.sh: examples of bash commands to use or generate the files stored in this archive.biosampleThis directory contains input and output files used to assign a “clinical” score to a BioSample report (…)
bldb_oxaFile in .fasta format of the reference OXA-family sequences from the Beta-lactamase Database (BLDB) used for annotation with the annotate.pl perl script from Bio::MUST modules.
genetic_environmentThis directory contains the list of bacterial assembly download links in .csv format to provide to GeneSpy and the list of contig accession numbers to download with the command-line efetch tool from the NCBI E-utilities.
local_refseq_dbThe list of the assembly accession numbers of the local RefSeq database built on 7th of December 2017.
ncbi_pathogenThis directory contains consolidated FASTA (.fasta) and TSV (.tab) files downloaded from the NCBI Pathogen Detection server (ftp://ftp.ncbi.nlm.nih.gov/pathogen/):
all-prot-nr.fastaall_bla.tabIt also contains files associated to class-D beta-lactamases (…)
oxa_familyThis directory contains the FASTA file bla_d.fasta with the 24,916 OXA-family protein selected with the ompa-pa.pl script and its deduplicated file clst95_bla_d.fasta and also the coordinates file class_d98.bb and the sequence accession identifier file class_d98.idl from ompa-pa.pl.
alignmentsThree alignments of OXA-family proteins are available (…)
treeThe mapper.idm is a TSV file that contains the short and corresponding long sequence identifiers used to rename sequences for booster and RAxML tree.
boosterThis directory contains raw output files obtained from the booster web server in NEWICK format. boosterweb_tbe_norm.nhis the final tree file.
consenseConsensus tree computed with consense (PHYLIP package) using the 100 replicate trees of RAxMLRAxML_bootstrap.classd-final-edit_188-RAXML-PROTGAMMALGF-100xRAPIDBP.
raxmlThis directory contains raw output files of RAxML in NEWICK format, computed from the reduced alignment classd-final-edit_188.fasta.
oxa_family_clustersThis directory contains alignment files in FASTA format and the corresponding .hmm profile files for non-singleton clusters (representative sequences) (…)
oxa_family_domainsThe 3510 unique OXA-family sequences and their corresponding taxonomy are available in FASTA format 3510_bla.fastaand TSV format 3510_bla.tax (…)
phylogenetic_clusteringThis directory contains a templatized R script mcl.script.R.tt used to compute phylogenetic clustering, the ladderized rooted OXA-family tree used by the R script and its associated traits file.
scriptsThis directory contains various perl scripts (…)
sql_dbThis directory contains the SQL files for the results database (…)
taxdump-20180208Mirror of the NCBI Taxonomy used in this study (downloaded on 8th of February 2018).