Class: metagenome assembly

URI: nmdc:MetagenomeAssembly

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Parents

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

Inherited from workflow execution activity:

Other properties

In Subsets: workflow subset