Pipeline reports

abricate

Table data

AMR table:
  • <abricate database>: Number of hits for a particular given database
../_images/abricate_table.png

Plot data

  • Sliding window AMR annotation: Provides annotation of Abricate hits for each database along the genome. This report component is only available when the pilon component was used downstream of abricate.
../_images/sliding_window_amr.png

assembly_mapping

Plot data

  • Data loss chart: Gives a trend of the data loss (in total number of base pairs) across components that may filter this data.
../_images/sparkline.png

Warnings

Assembly table:
  • When the number of contigs exceeds the threshold of 100 contigs per 1.5Mb.

Fails

Assembly table:
  • When the assembly size if smaller than 80% or larger than 150% of the expected genome size.

check_coverage

Table data

Quality control table:
  • Coverage: Estimated coverage based on the number of base pairs and the expected genome size.
../_images/quality_control_table.png

Warnings

Quality control table:
  • When the enconding and phred score cannot be guessed from the FastQ file(s).

Fails

Quality control table:
  • When the sample has lower estimated coverage than the provided coverage threshold.

chewbbaca

Table data

Chewbbaca table:
  • Table with the summary statistics of ChewBBACA allele calling, including the number of exact matches, inferred loci, loci not found, etc.
../_images/chewbbaca_table.png

dengue_typing

Table data

Typing table:
  • seqtyping: The sequence typing result (serotypy-genotype).
../_images/typing_table_dengue.png

fastqc

Plot data

  • Base sequence quality: The average quality score across the read length.
../_images/fastqc_base_sequence_quality.png
  • Sequence quality: Distribution of the mean sequence quality score.
../_images/fastqc_per_base_sequence_quality.png
  • Base GC content: Distribution of the GC content of each sequence.
../_images/fastqc_base_gc_content.png
  • Sequence length: Distribution of the read sequence length.
../_images/fastqc_sequence_length.png
  • Missing data: Normalized count of missing data across the read length.
../_images/fastqc_missing_data.png

Warnings

The following FastQC categories will issue a warning when they have a WARN flag:
  • Per base sequence quality.
  • Overrepresented sequences.
The following FastQC categories will issue a warning when do not have a PASS flag:
  • Per base sequence content.

Fails

The following FastQC categories will issue a fail when they have a FAIL flag:
  • Per base sequence quality.
  • Overrepresented sequences.
  • Sequence length distribution.
  • Per sequence GC content.
The following FastQC categories will issue a fail when the do not have a PASS flag:
  • Per base N content.
  • Adapter content.

fastqc_trimmomatic

Table data

Quality control table:
  • Trimmed (%): Percentage of trimmed base pairs.
../_images/quality_control_table.png

Plot data

  • Data loss chart: Gives a trend of the data loss (in total number of base pairs) across components that may filter this data.
../_images/sparkline.png

integrity_coverage

Table data

Quality control table:
  • Raw BP: Number of raw base pairs from the FastQ file(s).
  • Reads: Number of reads in the FastQ file(s)
  • Coverage: Estimated coverage based on the number of base pairs and the expected genome size.
../_images/quality_control_table.png

Plot data

  • Data loss chart: Gives a trend of the data loss (in total number of base pairs) across components that may filter this data.
../_images/sparkline.png

Warnings

Quality control table:
  • When the enconding and phred score cannot be guessed from the FastQ file(s).

Fails

Quality control table:
  • When the sample has lower estimated coverage than the provided coverage threshold.

mash_dist

Table data

Plasmids table:
  • Mash Dist: Number of plasmid hits
../_images/mash_dist_table.png

Plot data

  • Sliding window Plasmid annotation: Provides annotation of plasmid hits along the genome assembly. This report component is only available when the mash_dist component is used.
../_images/sliding_window_mash_dist.png

mlst

Table data

Typing table:
  • MLST species: The inferred species name.
  • MLST ST: The inferred sequence type.
../_images/typing_table.png

patho_typing

Table data

Typing table:
  • Patho_typing: The pathotyping result.
../_images/typing_table.png

pilon

Table data

Quality control table:
  • Contigs: Number of assembled contigs.
  • Assembled BP: Total number of assembled base pairs.
../_images/assembly_table_skesa.png

Plot data

  • Contig size distribution: Distribution of the size of each assembled contig.
../_images/contig_size_distribution.png
  • Sliding window coverage and GC content: Provides coverage and GC content metrics along the genome using a sliding window approach and two synchronised charts.
../_images/sliding_window_amr.png

Warnings

Quality control table:
  • When the enconding and phred score cannot be guessed from the FastQ file(s).

Fails

Quality control table:
  • When the sample has lower estimated coverage than the provided coverage threshold.

process_mapping

Table data

Read mapping table:
  • Reads: Number reads in the the FastQ file(s).
  • Unmapped: Number of unmapped reads
  • Mapped 1x: Number of reads that aligned, concordantly and discordantly, exactly 1 time
  • Mapped >1x: Number of reads that aligned, concordantly or disconrdantly, more than 1 times
  • Overall alignment rate (%): Overall alignment rate
../_images/read_mapping_remove_host.png

process_newick

Tree data

Phylogenetic reconstruction with bootstrap values for the provided tree.

../_images/phylogenetic_tree.png

process_skesa

Table data

Quality control table:
  • Contigs (skesa): Number of assembled contigs.
  • Assembled BP: Total number of assembled base pairs.
../_images/assembly_table_skesa.png

Warnings

Assembly table:
  • When the number of contigs exceeds the threshold of 100 contigs per 1.5Mb.

Fails

Assembly table:
  • When the assembly size if smaller than 80% or larger than 150% of the expected genome size.

process_spades

Table data

Quality control table:
  • Contigs (spades): Number of assembled contigs.
  • Assembled BP: Total number of assembled base pairs.
../_images/assembly_table_spades.png

Warnings

Assembly table:
  • When the number of contigs exceeds the threshold of 100 contigs per 1.5Mb.

Fails

Assembly table:
  • When the assembly size if smaller than 80% or larger than 150% of the expected genome size.

process_viral_assembly

Table data

Quality control table:
  • Contigs (SPAdes): Number of assembled contigs.
  • Assembled BP (SPAdes): Total number of assembled base pairs.
  • ORFs: Number of complete ORFs in the assembly.
  • Contigs (MEGAHIT): Number of assembled contigs.
  • Assembled BP (MEGAHIT): Total number of assembled base pairs.
../_images/assembly_table_viral_assembly.png

Fails

Assembly table:
  • When the assembly size if smaller than 80% or larger than 150% of the expected genome size.

seq_typing

Table data

Typing table:
  • seqtyping: The sequence typing result.
../_images/typing_table.png

sistr

Table data

Typing table:
  • sistr: The sequence typing result.
../_images/typing_table.png

trimmomatic

Table data

Quality control table:
  • Trimmed (%): Percentage of trimmed base pairs.
../_images/quality_control_table.png

Plot data

  • Data loss chart: Gives a trend of the data loss (in total number of base pairs) across components that may filter this data.
../_images/sparkline.png

true_coverage

Table data

Quality control table:
  • True Coverage: Estimated coverage based on read mapping on MLST genes.
../_images/quality_control_table.png

Fails

Quality control table:
  • When the sample has lower estimated coverage than the provided coverage threshold.