Pipeline reports¶
abricate¶
Table data¶
- AMR table:
- <abricate database>: Number of hits for a particular given database
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 ofabricate
.
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.
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.
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.
fastqc¶
Plot data¶
- Base sequence quality: The average quality score across the read length.
- Sequence quality: Distribution of the mean sequence quality score.
- Base GC content: Distribution of the GC content of each sequence.
- Sequence length: Distribution of the read sequence length.
- Missing data: Normalized count of missing data across the read length.
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¶
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.
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.
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.
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
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.
mlst¶
Table data¶
- Typing table:
- MLST species: The inferred species name.
- MLST ST: The inferred sequence type.
pilon¶
Table data¶
- Quality control table:
- Contigs: Number of assembled contigs.
- Assembled BP: Total number of assembled base pairs.
Plot data¶
- Contig size distribution: Distribution of the size of each assembled contig.
- Sliding window coverage and GC content: Provides coverage and GC content metrics along the genome using a sliding window approach and two synchronised charts.
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
process_skesa¶
Table data¶
- Quality control table:
- Contigs (skesa): Number of assembled contigs.
- Assembled BP: Total number of assembled base pairs.
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.
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.
Fails¶
- Assembly table:
- When the assembly size if smaller than 80% or larger than 150% of the expected genome size.