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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.14

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

This report has been generated by the Arcadia-Science/reads2genome analysis pipeline using the PacBio workflow.

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Report generated on 2023-08-09, 20:16 UTC based on data in: /tmp/nxf.kB242I4vX3

General Statistics

Showing ⁴⁸/₄₈ rows and ⁷/₉ columns.

Sample Name	N50 (Kbp)	Assembly Length (Mbp)	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs
acineobacter_baumanii_AYE			0.17%	0.0	0.0	99.9%	0.0%	0.0%	0.0
acineobacter_baumanii_AYE.flye.assembly	3938.8Kbp	3.9Mbp
bacillus_cereus_971			0.12%	0.0	0.0	100.0%	0.0%	0.1%	0.0
bacillus_cereus_971.flye.assembly	5416.5Kbp	5.4Mbp
bacillus_subtilis_w23			0.15%	0.0	0.0	99.9%	0.0%	0.0%	0.0
bacillus_subtilis_w23.flye.assembly	4045.6Kbp	4.0Mbp
burkholderia_cepacia_ucb717			0.14%	0.0	0.0	100.0%	0.0%	0.0%	0.0
burkholderia_cepacia_ucb717.flye.assembly	3397.8Kbp	8.6Mbp
burkholderia_multivorans_249			0.16%	0.0	0.0	100.0%	0.0%	0.0%	0.0
burkholderia_multivorans_249.flye.assembly	2473.2Kbp	7.0Mbp
enterococcus_faecalis_og1rf			0.15%	0.0	0.0	100.0%	0.0%	0.0%	0.0
enterococcus_faecalis_og1rf.flye.assembly	2739.6Kbp	2.7Mbp
escherichia_coli_h10407			0.17%	0.0	0.0	99.9%	0.0%	0.0%	0.0
escherichia_coli_h10407.flye.assembly	5153.4Kbp	5.4Mbp
escherichia_coli_k12_mg1655			0.15%	0.0	0.0	100.0%	0.0%	0.0%	0.0
escherichia_coli_k12_mg1655.flye.assembly	4639.0Kbp	4.6Mbp
helicobacter_pylori_j99			0.20%	0.0	0.0	99.9%	0.0%	0.0%	0.0
helicobacter_pylori_j99.flye.assembly	1645.7Kbp	1.6Mbp
klebsiella_pneumonia_baa2146			0.12%	0.0	0.0	100.0%	0.0%	0.0%	0.0
klebsiella_pneumonia_baa2146.flye.assembly	5435.7Kbp	5.8Mbp
listeria_monocytogenes_li2			0.14%	0.0	0.0	99.9%	0.0%	0.0%	0.0
listeria_monocytogenes_li2.flye.assembly	2951.0Kbp	3.0Mbp
listeria_monocytogenes_li23			0.14%	0.0	0.0	99.9%	0.0%	0.0%	0.0
listeria_monocytogenes_li23.flye.assembly	2979.7Kbp	3.0Mbp
methanocorpusculum_labreanum_z			0.18%	0.0	0.0	100.0%	0.0%	0.1%	0.0
methanocorpusculum_labreanum_z.flye.assembly	1805.0Kbp	1.8Mbp
neisseria_meningitidis_fam18			0.17%	0.0	0.0	99.8%	0.0%	0.1%	0.0
neisseria_meningitidis_fam18.flye.assembly	2194.9Kbp	2.2Mbp
neisseria_meningitidis_serogroup_b			0.16%	0.0	0.0	100.0%	0.0%	0.1%	0.0
neisseria_meningitidis_serogroup_b.flye.assembly	2305.8Kbp	2.3Mbp
rhodopseudomonas_palustris_cga009			0.15%	0.0	0.0	99.9%	0.0%	0.0%	0.0
rhodopseudomonas_palustris_cga009.flye.assembly	5459.2Kbp	5.5Mbp
salmonella_enterica_lt2			0.16%	0.0	0.0	100.0%	0.0%	0.0%	0.0
salmonella_enterica_lt2.flye.assembly	4857.5Kbp	5.0Mbp
salmonella_enterica_ty2			0.15%	0.0	0.0	100.0%	0.0%	0.2%	0.0
salmonella_enterica_ty2.flye.assembly	4792.0Kbp	4.8Mbp
staphylococcus_aureus_USA300_TCH1516			0.11%	0.0	0.0	97.6%	0.0%	0.0%	0.0
staphylococcus_aureus_USA300_TCH1516.flye.assembly	2878.9Kbp	2.9Mbp
staphylococcus_aureus_seattle1945			0.12%	0.0	0.0	99.9%	0.0%	0.0%	0.0
staphylococcus_aureus_seattle1945.flye.assembly	2778.9Kbp	2.8Mbp
streptococcus_pyogenes_bruno			0.11%	0.0	0.0	100.0%	0.0%	0.1%	0.0
streptococcus_pyogenes_bruno.flye.assembly	1839.0Kbp	1.8Mbp
thermanaerovibrio_acidaminovorans_dsm6589			0.14%	0.0	0.0	99.1%	0.0%	0.1%	0.0
thermanaerovibrio_acidaminovorans_dsm6589.flye.assembly	1850.2Kbp	1.9Mbp
treponema_denticola_a			0.18%	0.0	0.0	99.9%	0.0%	0.0%	0.0
treponema_denticola_a.flye.assembly	2842.7Kbp	2.8Mbp
vibrio_parahaemolyticus_eb101			0.13%	0.0	0.0	100.0%	0.0%	0.0%	0.0
vibrio_parahaemolyticus_eb101.flye.assembly	3165.6Kbp	5.2Mbp

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly (kilo base pairs)	`N50`	None
\|\|	QUAST	Assembly Length (Mbp)	The total number of bases in the assembly (Mbp).	`Total length`	None
\|\|	Samtools	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`error_rate`	None
\|\|	Samtools	M Non-Primary	Non-primary alignments (millions)	`non-primary_alignments`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`reads_mapped`	read_count
\|\|	Samtools	% Mapped	% Mapped Reads	`reads_mapped_percent`	None
\|\|	Samtools	% Proper Pairs	% Properly Paired Reads	`reads_properly_paired_percent`	None
\|\|	Samtools	% MapQ 0 Reads	% of Reads that are Ambiguously Placed (MapQ=0)	`reads_MQ0_percent`	None
\|\|	Samtools	M Total seqs	Total sequences in the bam file (millions)	`raw_total_sequences`	read_count

NanoStat

NanoStat various statistics from a long read sequencing dataset in fastq, bam or sequencing summary format.DOI: 10.1093/bioinformatics/bty149.

Fastq stats

NanoStat statistics from FastQ files.

Showing ²⁴/₂₄ rows and ⁵/₇ columns.

Sample Name	Median length	Mean length	Read N50	Median Qual	Mean Qual	# Reads (K)	Total Bases (Mb)
acineobacter_baumanii_AYE_nanoplot_stats	8354 bp	8506 bp	9130 bp	38.1	40.2	15.2	129.0
bacillus_cereus_971_nanoplot_stats	6064 bp	6190 bp	7501 bp	41.3	48.7	24.9	154.0
bacillus_subtilis_w23_nanoplot_stats	8810 bp	8945 bp	9674 bp	36.7	38.5	18.3	163.7
burkholderia_cepacia_ucb717_nanoplot_stats	7994 bp	8124 bp	8755 bp	36.9	39.4	45.4	368.7
burkholderia_multivorans_249_nanoplot_stats	8635 bp	8770 bp	9585 bp	36.0	38.7	27.7	242.9
enterococcus_faecalis_og1rf_nanoplot_stats	7717 bp	7763 bp	8728 bp	37.8	41.0	13.1	101.4
escherichia_coli_h10407_nanoplot_stats	8472 bp	8483 bp	9431 bp	37.5	40.4	26.4	223.7
escherichia_coli_k12_mg1655_nanoplot_stats	9006 bp	9060 bp	10059 bp	36.7	39.6	14.6	132.3
helicobacter_pylori_j99_nanoplot_stats	7844 bp	7891 bp	8752 bp	35.3	37.0	6.8	53.9
klebsiella_pneumonia_baa2146_nanoplot_stats	6565 bp	6598 bp	7385 bp	40.0	44.6	28.1	185.2
listeria_monocytogenes_li23_nanoplot_stats	8180 bp	8228 bp	9069 bp	37.8	40.5	13.0	107.4
listeria_monocytogenes_li2_nanoplot_stats	8106 bp	8067 bp	9209 bp	37.4	40.8	7.1	57.5
methanocorpusculum_labreanum_z_nanoplot_stats	6933 bp	6999 bp	8068 bp	37.7	42.0	7.0	48.7
neisseria_meningitidis_fam18_nanoplot_stats	7694 bp	7744 bp	8693 bp	37.2	40.4	9.6	74.4
neisseria_meningitidis_serogroup_b_nanoplot_stats	8086 bp	8164 bp	8992 bp	36.8	39.2	9.7	79.2
rhodopseudomonas_palustris_cga009_nanoplot_stats	7800 bp	7762 bp	9094 bp	37.6	43.0	23.1	179.6
salmonella_enterica_lt2_nanoplot_stats	9114 bp	9254 bp	10070 bp	36.1	38.1	20.1	186.4
salmonella_enterica_ty2_nanoplot_stats	7639 bp	7577 bp	8841 bp	38.3	42.9	23.6	179.1
staphylococcus_aureus_USA300_TCH1516_nanoplot_stats	7378 bp	7490 bp	8195 bp	40.2	44.0	15.3	114.6
staphylococcus_aureus_seattle1945_nanoplot_stats	7762 bp	7684 bp	8761 bp	39.1	43.7	7.1	54.5
streptococcus_pyogenes_bruno_nanoplot_stats	6787 bp	6819 bp	7752 bp	40.1	44.9	10.7	73.3
thermanaerovibrio_acidaminovorans_dsm6589_nanoplot_stats	2939 bp	3778 bp	4769 bp	42.2	52.1	14.5	54.8
treponema_denticola_a_nanoplot_stats	8388 bp	8436 bp	9314 bp	35.5	37.4	14.1	119.1
vibrio_parahaemolyticus_eb101_nanoplot_stats	8811 bp	8942 bp	9759 bp	37.9	40.6	20.1	180.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	NanoStat	Median length	Median read length (bp)	`Median read length_fastq`	nucleotides
\|\|	NanoStat	Mean length	Mean read length (bp)	`Mean read length_fastq`	nucleotides
\|\|	NanoStat	Read N50	Read length N50	`Read length N50_fastq`	None
\|\|	NanoStat	Median Qual	Median read quality (Phred scale)	`Median read quality_fastq`	phred_score
\|\|	NanoStat	Mean Qual	Mean read quality (Phred scale)	`Mean read quality_fastq`	phred_score
\|\|	NanoStat	# Reads (K)	Number of reads (thousands)	`Number of reads_fastq`	long_read_count
\|\|	NanoStat	Total Bases (Mb)	Total bases (millions)	`Total bases_fastq`	base_count

Reads by quality

Read counts categorised by read quality (phred score).

Sequencing machines assign each generated read a quality score using the Phred scale. The phred score represents the liklelyhood that a given read contains errors. So, high quality reads have a high score.

Data may come from NanoPlot reports generated with sequencing summary files or alignment stats. If a sample has data from both, the sequencing summary is preferred.

QUAST

QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

Assembly Statistics

Showing ²⁴/₂₄ rows and ⁴/₄ columns.

Sample Name	N50 (Kbp)	L50 (K)	Largest contig (Kbp)	Length (Mbp)
acineobacter_baumanii_AYE.flye.assembly	3938.8Kbp	0.0K	3938.8Kbp	3.9Mbp
bacillus_cereus_971.flye.assembly	5416.5Kbp	0.0K	5416.5Kbp	5.4Mbp
bacillus_subtilis_w23.flye.assembly	4045.6Kbp	0.0K	4045.6Kbp	4.0Mbp
burkholderia_cepacia_ucb717.flye.assembly	3397.8Kbp	0.0K	3781.2Kbp	8.6Mbp
burkholderia_multivorans_249.flye.assembly	2473.2Kbp	0.0K	3448.5Kbp	7.0Mbp
enterococcus_faecalis_og1rf.flye.assembly	2739.6Kbp	0.0K	2739.6Kbp	2.7Mbp
escherichia_coli_h10407.flye.assembly	5153.4Kbp	0.0K	5153.4Kbp	5.4Mbp
escherichia_coli_k12_mg1655.flye.assembly	4639.0Kbp	0.0K	4639.0Kbp	4.6Mbp
helicobacter_pylori_j99.flye.assembly	1645.7Kbp	0.0K	1645.7Kbp	1.6Mbp
klebsiella_pneumonia_baa2146.flye.assembly	5435.7Kbp	0.0K	5435.7Kbp	5.8Mbp
listeria_monocytogenes_li2.flye.assembly	2951.0Kbp	0.0K	2951.0Kbp	3.0Mbp
listeria_monocytogenes_li23.flye.assembly	2979.7Kbp	0.0K	2979.7Kbp	3.0Mbp
methanocorpusculum_labreanum_z.flye.assembly	1805.0Kbp	0.0K	1805.0Kbp	1.8Mbp
neisseria_meningitidis_fam18.flye.assembly	2194.9Kbp	0.0K	2194.9Kbp	2.2Mbp
neisseria_meningitidis_serogroup_b.flye.assembly	2305.8Kbp	0.0K	2305.8Kbp	2.3Mbp
rhodopseudomonas_palustris_cga009.flye.assembly	5459.2Kbp	0.0K	5459.2Kbp	5.5Mbp
salmonella_enterica_lt2.flye.assembly	4857.5Kbp	0.0K	4857.5Kbp	5.0Mbp
salmonella_enterica_ty2.flye.assembly	4792.0Kbp	0.0K	4792.0Kbp	4.8Mbp
staphylococcus_aureus_USA300_TCH1516.flye.assembly	2878.9Kbp	0.0K	2878.9Kbp	2.9Mbp
staphylococcus_aureus_seattle1945.flye.assembly	2778.9Kbp	0.0K	2778.9Kbp	2.8Mbp
streptococcus_pyogenes_bruno.flye.assembly	1839.0Kbp	0.0K	1839.0Kbp	1.8Mbp
thermanaerovibrio_acidaminovorans_dsm6589.flye.assembly	1850.2Kbp	0.0K	1850.2Kbp	1.9Mbp
treponema_denticola_a.flye.assembly	2842.7Kbp	0.0K	2842.7Kbp	2.8Mbp
vibrio_parahaemolyticus_eb101.flye.assembly	3165.6Kbp	0.0K	3165.6Kbp	5.2Mbp

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly.	`N50`	None
\|\|	QUAST	L50 (K)	L50 is the number of contigs larger than N50, i.e. the minimum number of contigs comprising 50% of the total assembly length.	`L50`	None
\|\|	QUAST	Largest contig (Kbp)	The size of the largest contig of the assembly	`Largest contig`	None
\|\|	QUAST	Length (Mbp)	The total number of bases in the assembly.	`Total length`	None

Number of Contigs

This plot shows the number of contigs found for each assembly, broken down by length.

BUSCO

BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

Lineage: bacteria_odb10

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

Percent Mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Alignment metrics

This module parses the output from samtools stats. All numbers in millions.

Arcadia-Science/reads2genome Software Versions

are collected at run time from the software output.

Process Name	Software	Version
`BUSCO`	`busco`	`5.4.3`
`CHECK_SAMPLESHEET`	`python`	`3.9.5`
`CUSTOM_DUMPSOFTWAREVERSIONS`	`python`	`3.11.0`
	`yaml`	`6.0`
`FLYE`	`flye`	`2.9-b1768`
`MINIMAP2_INDEX`	`minimap2`	`2.24-r1122`
`NANOPLOT`	`nanoplot`	`1.41.0`
`QUAST`	`quast`	`5.2.0`
`SAMTOOLS_STATS`	`samtools`	`1.17`
`Workflow`	`Arcadia-Science/reads2genome`	`1.0dev`
	`Nextflow`	`23.04.2`

Arcadia-Science/reads2genome Workflow Summary

- this information is collected when the pipeline is started.

Core Nextflow options

revision: main
runName: cranky_babbage
containerEngine: docker
launchDir: /
workDir: /nf-hifi2genome/scratch/5GkUCm3DuLbKSW
projectDir: /.nextflow/assets/Arcadia-Science/reads2genome
userName: root
profile: docker
configFiles: /.nextflow/assets/Arcadia-Science/reads2genome/nextflow.config, /nextflow.config

input_output_options

input: s3://nf-test-datasets/reads2genome/2023-08-09-pbhifi-test-full-samplesheet.csv
outdir: s3://nf-test-datasets/reads2genome/pb_hifi_test
platform: pacbio

busco_options

lineage: bacteria_odb10

Email options

email: [email protected]
from_email: [email protected]

Max job request options

max_memory: 400.GB

multiqc_options

multiqc_title: PacBio HiFi Microbes Full Test
multiqc_methods_description: N/A
multiqc_logo: N/A
multiqc_config: N/A

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General Statistics

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NanoStat fastq: Columns

Reads by quality Help

QUAST

Assembly Statistics

Quast Table: Columns

Number of Contigs

BUSCO

Lineage: bacteria_odb10

Samtools

Percent Mapped Help

Alignment metrics

Arcadia-Science/reads2genome Software Versions

Arcadia-Science/reads2genome Workflow Summary

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