Class: metagenome assembly
Parents
is_a: WorkflowExecutionActivity - Represents an instance of an execution of a particular workflow
Referenced by Class
Attributes
Own
asm_score 0..1
Description: A score for comparing metagenomic assembly quality from same sample.
Range: Float
scaffolds 0..1
Description: Total sequence count of all scaffolds.
Range: Float
scaf_logsum 0..1
Description: The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase
Range: Float
scaf_powsum 0..1
Description: Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
Range: Float
scaf_max 0..1
Description: Maximum scaffold length.
Range: Float
scaf_bp 0..1
Description: Total size in bp of all scaffolds.
Range: Float
scaf_N50 0..1
Description: Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.
Range: Float
scaf_N90 0..1
Description: Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.
Range: Float
scaf_L50 0..1
Description: Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.
Range: Float
scaf_L90 0..1
Description: The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.
Range: Float
scaf_n_gt50K 0..1
Description: Total sequence count of scaffolds greater than 50 KB.
Range: Float
scaf_l_gt50K 0..1
Description: Total size in bp of all scaffolds greater than 50 KB.
Range: Float
scaf_pct_gt50K 0..1
Description: Total sequence size percentage of scaffolds greater than 50 KB.
Range: Float
contigs 0..1
Description: The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase
Range: Float
contig_bp 0..1
Description: Total size in bp of all contigs.
Range: Float
ctg_N50 0..1
Description: Given a set of contigs, each with its own length, the N50 count is defined as the smallest number of contigs whose length sum makes up half of genome size.
Range: Float
ctg_L50 0..1
Description: Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.
Range: Float
ctg_N90 0..1
Description: Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.
Range: Float
ctg_L90 0..1
Description: The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.
Range: Float
ctg_logsum 0..1
Description: Maximum contig length.
Range: Float
ctg_powsum 0..1
Description: Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
Range: Float
ctg_max 0..1
Description: Maximum contig length.
Range: Float
gap_pct 0..1
Description: The gap size percentage of all scaffolds.
Range: Float
gc_std 0..1
Description: Standard deviation of GC content of all contigs.
Range: Float
gc_avg 0..1
Description: Average of GC content of all contigs.
Range: Float
num_input_reads 0..1
Description: The sequence count number of input reads for assembly.
Range: Float
num_aligned_reads 0..1
Description: The sequence count number of input reads aligned to assembled contigs.
Range: Float
INSDC assembly identifiers 0..1
Range: String
Inherited from workflow execution activity:
id 1..1
Description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
Range: String
name 0..1
Description: A human readable label for an entity
Range: String
used 0..1
Range: String
workflow execution activity➞execution resource 1..1
Description: Example: NERSC-Cori
Range: String
workflow execution activity➞git url 1..1
Description: Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1
Range: String
workflow execution activity➞has input 1..*
Description: An input to a process.
Range: NamedThing
workflow execution activity➞has output 1..*
Description: An output biosample to a processing step
Range: NamedThing
part of 0..*
Description: Links a resource to another resource that either logically or physically includes it.
Range: NamedThing
workflow execution activity➞type 1..1
Description: An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.
Range: String
Example: nmdc:Biosample None
Example: nmdc:Study None
workflow execution activity➞was associated with 0..1
Description: the agent/entity associated with the generation of the file
Range: WorkflowExecutionActivity
workflow execution activity➞started at time 1..1
Range: Datetime
workflow execution activity➞ended at time 1..1
Range: Datetime
workflow execution activity➞was informed by 1..1
Range: Activity
Other properties
In Subsets: | workflow subset |