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Subset: Sequencing

URI: Sequencing

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc

Classes in subset

Class Description

Slots in subset

Slot Description
adapters Adapters provide priming sequences for both amplification and sequencing of t...
annot Tool used for annotation, or for cases where annotation was provided by a com...
assembly_name Name/version of the assembly provided by the submitter that is used in the ge...
assembly_qual The assembly quality category is based on sets of criteria outlined for each ...
assembly_software Tool(s) used for assembly, including version number and parameters
associated_resource A related resource that is referenced, cited, or otherwise associated to the ...
bin_param The parameters that have been applied during the extraction of genomes from m...
bin_software Tool(s) used for the extraction of genomes from metagenomic datasets, where p...
chimera_check Tool(s) used for chimera checking, including version number and parameters, t...
compl_appr The approach used to determine the completeness of a given genomic assembly, ...
compl_score Completeness score is typically based on either the fraction of markers found...
compl_software Tools used for completion estimate, i
contam_score The contamination score is based on the fraction of single-copy genes that ar...
contam_screen_input The type of sequence data used as input
contam_screen_param Specific parameters used in the decontamination sofware, such as reference da...
decontam_software Tool(s) used in contamination screening
detec_type Type of UViG detection
feat_pred Method used to predict UViGs features such as ORFs, integration site, etc
host_pred_appr Tool or approach used for host prediction
host_pred_est_acc For each tool or approach used for host prediction, estimated false discovery...
lib_layout Specify whether to expect single, paired, or other configuration of reads
lib_reads_seqd Total number of clones sequenced from the library
lib_screen Specific enrichment or screening methods applied before and/or after creating...
lib_size Total number of clones in the library prepared for the project
lib_vector Cloning vector type(s) used in construction of libraries
mag_cov_software Tool(s) used to determine the genome coverage if coverage is used as a binnin...
mid Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...
nucl_acid_amp A link to a literature reference, electronic resource or a standard operating...
nucl_acid_ext A link to a literature reference, electronic resource or a standard operating...
number_contig Total number of contigs in the cleaned/submitted assembly that makes up a giv...
otu_class_appr Cutoffs and approach used when clustering species-level OTUs
otu_db Reference database (i
otu_seq_comp_appr Tool and thresholds used to compare sequences when computing "species-level" ...
pcr_cond Description of reaction conditions and components of PCR in the form of 'init...
pcr_primers PCR primers that were used to amplify the sequence of the targeted gene, locu...
pred_genome_struc Expected structure of the viral genome
pred_genome_type Type of genome predicted for the UViG
reassembly_bin Has an assembly been performed on a genome bin extracted from a metagenomic a...
ref_db List of database(s) used for ORF annotation, along with version number and re...
sc_lysis_approach Method used to free DNA from interior of the cell(s) or particle(s)
sc_lysis_method Name of the kit or standard protocol used for cell(s) or particle(s) lysis
seq_meth Sequencing machine used
seq_quality_check Indicate if the sequence has been called by automatic systems (none) or under...
sim_search_meth Tool used to compare ORFs with database, along with version and cutoffs used
sop Standard operating procedures used in assembly and/or annotation of genomes, ...
sort_tech Method used to sort/isolate cells or particles of interest
target_gene Targeted gene or locus name for marker gene studies
target_subfragment Name of subfragment of a gene or locus
tax_class Method used for taxonomic classification, along with reference database used,...
tax_ident The phylogenetic marker(s) used to assign an organism name to the SAG or MAG
trna_ext_software Tools used for tRNA identification
trnas The total number of tRNAs identified from the SAG or MAG
vir_ident_software Tool(s) used for the identification of UViG as a viral genome, software or pr...
wga_amp_appr Method used to amplify genomic DNA in preparation for sequencing
wga_amp_kit Kit used to amplify genomic DNA in preparation for sequencing
x16s_recover Can a 16S gene be recovered from the submitted SAG or MAG?
x16s_recover_software Tools used for 16S rRNA gene extraction

Enumerations in subset

Enumeration Description