Overview

Edit a predefined set of Laboratory Procedure Details

The Procedure Details are used to document the laboratory procedure, the assembly procedure, the target scan procedure, and the target QC procedure.

The laboratory and assembly procedure details can be predefined and managed using the menu item Options | Procedure Details. If a new Sample is created from genome data Procedure Details can be assigned to Samples. In addition, the laboratory and assembly procedure details of an existing Sample can be edited.

The procedure details are also shown above the procedure statistics in the Procedure tab of the Sample Overview and they can be exported like epidemiological data fields. The laboratory and assembly procedure details can also be exported to and imported from SPEC Files.

Laboratory Procedure Details

The laboratory procedure details must be specified manually for an input file or defined once in a pipeline script for all following processed samples.

Field	Description	Submission
Nucleic Acid Extraction	Link to a literature reference, electronic resource or a standard operating procedure (SOP)
Library Source	Library source used (e.g., genomic, transcriptomic, cDNA, or metagenomic)
Library Strategy	Library strategy used (e.g., WGS, WGA, WXS, or RNA-Seq)
Library Selection	Library selection used (e.g., random, PCR, random PCR, orRT-PCR)
Library Construction Method	Library construction method used If set, this field has an effect on the coloring of the Avg. Coverage
Library Amplification Method	Library amplification method used
Sequencing Protocol	Sequencing protocol used (e.g., single-end reads, paired-end reads, or mate-pair reads) This field is required in assembling pipelines to configure the assembler
Library Insert Size	Library insert size in base pairs (excluding adaptors and/or primers)	¹⁾
Sequencing Length	Number of bases of insert sequenced	¹⁾
Sequencing Vendor	Sequencing platform producer (e.g., Illumina, PacBio, or Oxford Nanopore) This field is required in assembling pipelines to choose and configure the assembler
Sequencing Platform	Sequencing platform used (e.g., MiSeq, Sequel, or MinION)
Sequencing Run ID	ID of the sequencing run that was imported and stored as Sequencing Run Details when processing the sequence data
Sequencing Run QC	Overall result for the quality control of the Sequencing Run Details (succeeded or warning)

This field is submitted (required) and published on EMBL-EBI ENA when the Sample is submitted.
¹⁾ Only required for EMBL-EBI ENA if paired-end data is submitted.

Assembly Procedure Details

The laboratory procedure details can be specified manually for an input file or defined once in a pipeline script for all following processed samples. If the pipeline performs an assembling (de novo or mapping), any existing values will be overwritten by the actually used assembly procedure details.

Field	Description	Submission
Assembly pre-processing	Coverage downsampeled and/or trimmed by quality (window and QV) or adapter sequences
Assembly type	General assembly approach (de-novo or mapping)
Mapping reference genome	NCBI accession number of reference genome against which raw read data were mapped
Assembler	Software used for assembly
Assembler version	Version of software used for assembly
Assembler parameters	Assembler parameters used for assembly
Sequencing comment	Additional information regarding laboratory and assembly meta-data
Downsampled to Coverage¹⁾	Expected genome coverage that was used to calculate the ratio for random downsampling
Expected Genome Size for Downsampling¹⁾	Expected genome size that was used to calculate the ratio for random downsampling
Quality Trimming¹⁾	Parameters that were used for quality trimming of reads

¹⁾ not editable and only available if assembled with a SeqSphere+ pipeline

Target Scan Procedure Details

The target scan procedure details are stored as one text field. In contrast to the laboratory and assembly details, these details are not editable and never submitted to cgMLST.org. They are always automatically filled in by SeqSphere+. They are defined in the Task Procedure settings of the Task Template.

Example:

Ridom SeqSphere+ version 3.4.0_(2016-10)
BLAST version 2.2.12
Ignore contigs shorter than 200 bases

Scan for ref.-seqs. of L. monocytogenes cgMLST v2.1
  ref.-seq. scan BLASTN options: word size=11, mismatch=-1, match=1, gap open=5, gap ext.=2
  scan thresholds for hit: identity>=90, aligned=100
  require unique match found within the scan thresholds

Scan for ref.-seqs. of L. monocytogenes Accessory v2.0
  ref.-seq. scan BLASTN options: word size=11, mismatch=-1, match=1, gap open=5, gap ext.=2
  scan thresholds for hit: identity>=90, aligned=100
  require unique match found within the scan thresholds

Scan for ref.-seqs. and alleles of L. monocytogenes MLST v1.0
  ref.-seq. scan BLASTN options: word size=11, mismatch=-1, match=1, gap open=5, gap ext.=2
  allele scan BLASTN options: word size=11, mismatch=-1, match=1, gap open=5, gap ext.=2
  scan thresholds for hit: identity>=90, aligned>=99
  require unique match found within the scan thresholds

Target QC Procedure Details

The target QC procedure details are stored as one text field. In contrast to the laboratory and assembly details, these details are not editable and never submitted to cgMLST.org. They are always automatically filled in by SeqSphere+. They are defined in the Target QC Procedure settings of the Task Template.