ContentsOverviewSPEC files can be used in SeqSphere to export and import Metadata together with sequence data files. There are different purposed where they are useful:
SPEC File FormatThe SPEC file for a sample must have the same name as the input sequence file (e.g., FASTA or FASTQ) but with the file name extension ".spec". If a specific filenaming is used in a pipeline, the SPEC file may also have the name of the sample ID. Additionally, a SPEC file can also be defined for all sequence files of its directory, if it is named "sequence_specification.spec". If multiple SPEC files are found for a sample, they are merged together. The content of a SPEC file is plain text (UTF-8) where each line holds a single field and value pair, in the format: field=value (e.g., Epi Metadata Fieldsef.Sample.alias_id ef.Sample.isolationDate ef.Sample.receiptDate ef.Sample.sample_id_of_collector ef.Sample.sender ef.Sample.comment ef.Sample.modifiedDate ef.Sample.createdDate ef.Sample.submittedDate ef.Sample.downloaded_from ef.Sample.submitted_to ef.Source.source_type ef.Source.source_subtype ef.Source.host ef.Source.host_age ef.Source.host_sex ef.Source.host_disease ef.Source.isolation_source ef.Source.isolation_country ef.Source.isolation_state ef.Source.isolation_city ef.Source.isolation_zip ef.Source.isolation_lat_long ef.Source.lat_long_resolution ef.Source.cluster_outbreak ef.Source.epi_info ef.Source.case_id ef.Source.ecdc_case_id ef.Characteristic.genus ef.Characteristic.species ef.Characteristic.subspecies ef.Characteristic.strain ef.Characteristic.genotype ef.Characteristic.serotype ef.Characteristic.pathotype ef.Characteristic.identification_method ef.Characteristic.identification_kit_vendor ef.Characteristic.culture_collection ef.Characteristic.pubmed_id ef.Characteristic.study ef.Characteristic.ncbi_accession ef.Characteristic.experiment_accession ef.Characteristic.sample_accession ef.Characteristic.study_accession ef.Report.report_comment Procedure Details and Statitistics Fieldspf.library_source pf.library_strategy pf.sequencing_protocol pf.sequencing_vendor pf.assembly_pre-processing pf.assembly_type pf.assembler pf.assembler_version pf.assembler_parameters pf.assembly_post-processing pf.expected_genome_size_for_downsampling pf.downsampled_to_coverage pf.top_species_match pf.top_species_match_identity pf.top_species_match_shared-hashes pf.contamination_check_result pf.fastqc_per_base_sequence_quality_(forward_reads) pf.fastqc_per_base_sequence_quality_(reverse_reads) pf.fastqc_adapter_content pf.avg._coverage_(unassembled) pf.avg._coverage_(processed,_unassembled) pf.avg._read_length_(unassembled) pf.avg._read_length_(processed,_unassembled) pf.read_count_(unassembled) pf.read_count_(processed,_unassembled) pf.read_base_count_(unassembled) pf.read_base_count_(processed,_unassembled) pf.contig_count_(assembled) pf.n50_(assembled) pf.read_count_(assembled) pf.read_fwd_count_(assembled) pf.read_rev_count_(assembled) pf.consensus_base_count_(assembled) pf.approximated_genome_size_(mbases) pf.max_contig_length_(assembled) pf.min_contig_length_(assembled) pf.avg._contig_length_(assembled) pf.avg._coverage_(assembled) pf.read_base_count_(assembled) Paths to Raw Read Files Fieldsfl.reads.1 fl.reads.2 |