Toolbox

MultiQC Toolbox

Highlight Samples

Regex mode off

Rename Samples

Click here for bulk input.

Paste two columns of a tab-delimited table here (eg. from Excel).

First column should be the old name, second column the new name.

Regex mode off

Show / Hide Samples

Regex mode off

Export Plots

Images
Data

Aspect ratio

Plot scaling

Download the raw data used to create the plots in this report below:

Format:

Note that additional data was saved in multiqc_data when this report was generated.

Choose Plots

If you use plots from MultiQC in a publication or presentation, please cite:

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

Save Settings

You can save the toolbox settings for this report to the browser.

Load Settings

Choose a saved report profile from the dropdown box below:

Tool Citations

Please remember to cite the tools that you use in your analysis.

To help with this, you can download publication details of the tools mentioned in this report:

About MultiQC

This report was generated using MultiQC, version 1.13.dev0

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

GMH/cleanup
A prescreening pipeline for GMH Metagenome studies

MultiQC reports summarise analysis results about host contamination and QC

Contact E-mail: andrea.telatin@quadram.ac.uk
Application Type: GMH Metagenomics
Project Type: Whole Metagenome Sequencing
Sequencing Setup: 2x150bp

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Report generated on 2023-01-06, 16:17 UTC

General Statistics

Showing ⁵⁰/₅₀ rows and ⁷/₉ columns.

Sample Name	% Blautia obeum	% Top 5 Species	% Unclassified	% Duplication	% > Q30	Mb Q30 bases	GC content	% PF	% Adapter
100-A_S81_L001	8.4%	9.9%	90.0%	0.1%	92.5%	91.2	45.0%	99.6%	1.7%
101-A_S82_L001	2.8%	4.8%	92.8%	0.2%	91.1%	93.5	48.8%	99.3%	2.7%
102-A_S83_L001	3.7%	4.9%	94.8%	0.2%	93.6%	128.7	42.7%	99.3%	1.5%
103-A_S84_L001	2.8%	11.4%	88.5%	0.5%	93.5%	48.8	47.7%	99.2%	2.0%
104-A_S85_L001	0.9%	21.7%	78.2%	1.3%	95.8%	19.6	43.5%	93.7%	0.5%
105-A_S86_L001	3.6%	5.3%	94.4%	0.2%	92.4%	157.4	48.4%	99.2%	2.2%
106-A_S87_L001	2.7%	5.2%	94.4%	0.1%	90.7%	48.6	46.6%	99.5%	1.6%
107-A_S88_L001	1.3%	10.3%	89.4%	0.1%	91.2%	183.4	49.5%	99.5%	3.0%
108-A_S89_L001	5.1%	7.2%	91.8%	0.4%	90.0%	22.6	43.0%	98.4%	1.6%
109-A_S90_L001	3.9%	25.1%	74.7%	0.2%	90.8%	99.4	50.1%	99.3%	2.5%
110-A_S91_L001	0.4%	11.0%	87.9%	0.2%	94.5%	181.2	44.8%	99.5%	1.4%
111-A_S92_L001	1.7%	8.5%	90.4%	0.2%	93.2%	147.2	48.0%	99.5%	2.0%
112-A_S93_L001	2.6%	48.5%	51.4%	0.2%	90.4%	118.2	50.6%	99.4%	2.2%
113-A_S94_L001	1.2%	4.1%	94.8%	0.6%	92.0%	39.3	45.9%	97.9%	1.8%
1_S1_L001	0.9%	1.8%	98.1%	0.2%	94.3%	170.0	49.4%	99.4%	0.0%
2_S2_L001	2.8%	3.2%	96.7%	0.5%	96.4%	33.8	45.5%	98.8%	0.0%
3_S3_L001	0.4%	6.6%	93.3%	1.0%	92.6%	46.0	40.5%	98.5%	0.1%
4_S4_L001	1.0%	3.4%	96.5%	0.3%	92.9%	53.7	43.6%	99.3%	0.0%
5_S5_L001	2.0%	4.1%	95.7%	0.4%	93.0%	91.2	42.1%	99.3%	0.1%
69-A_S50_L001	2.1%	5.5%	93.5%	0.1%	90.2%	53.6	50.1%	99.8%	2.8%
70-A_S51_L001	4.0%	8.2%	91.3%	0.1%	91.8%	91.0	48.1%	99.8%	2.4%
71-A_S52_L001	2.1%	15.4%	83.9%	0.1%	90.9%	74.9	48.7%	99.7%	2.7%
72-A_S53_L001	1.8%	9.7%	90.0%	0.1%	92.7%	64.2	47.4%	99.7%	2.1%
73-A_S54_L001	1.9%	8.0%	91.2%	0.1%	90.9%	126.9	49.1%	99.6%	2.7%
74-A_S55_L001	2.4%	4.6%	95.2%	0.1%	91.8%	114.3	48.2%	99.7%	2.5%
75-A_S56_L001	2.5%	4.4%	95.4%	0.2%	94.5%	113.5	46.0%	99.3%	1.6%
76-A_S57_L001	5.6%	5.9%	93.9%	0.1%	91.3%	22.1	44.0%	99.8%	2.1%
77-A_S58_L001	2.4%	22.2%	77.6%	0.2%	92.3%	54.2	45.9%	99.3%	2.0%
78-A_S59_L001	3.5%	6.2%	93.6%	0.2%	93.6%	164.3	48.2%	99.5%	1.8%
79-A_S60_L001	2.7%	7.4%	91.7%	0.1%	89.2%	90.9	49.3%	99.5%	1.7%
80-A_S61_L001	3.1%	16.5%	83.2%	0.1%	92.3%	66.7	46.6%	99.7%	2.3%
81-A_S62_L001	3.2%	5.0%	94.6%	0.1%	91.7%	60.6	48.0%	99.5%	2.3%
82-A_S63_L001	3.3%	5.8%	94.0%	0.2%	92.4%	159.7	46.2%	99.4%	2.4%
83-A_S64_L001	4.7%	11.2%	88.7%	0.1%	92.0%	116.0	44.2%	99.8%	2.0%
84-A_S65_L001	2.3%	3.7%	96.1%	0.2%	93.4%	38.7	45.5%	99.3%	1.9%
85-A_S66_L001	3.6%	6.1%	93.6%	0.2%	90.4%	151.1	47.8%	99.4%	2.8%
86-A_S67_L001	4.8%	7.7%	92.2%	0.2%	94.2%	48.8	42.8%	99.2%	1.4%
87-A_S68_L001	2.8%	7.0%	92.8%	0.2%	92.5%	146.4	47.8%	99.4%	2.0%
88-A_S69_L001	3.1%	15.9%	83.8%	0.2%	91.4%	107.6	48.5%	99.4%	2.7%
89-A_S70_L001	1.9%	12.4%	87.3%	0.1%	90.8%	132.3	51.1%	99.7%	2.9%
90-A_S71_L001	1.2%	15.1%	84.3%	0.2%	92.6%	173.8	46.1%	99.5%	2.3%
91-A_S72_L001	3.3%	7.8%	91.8%	0.2%	92.5%	216.3	45.8%	99.6%	1.9%
92-A_S73_L001	4.0%	7.2%	92.5%	0.2%	93.2%	154.8	48.8%	99.5%	2.3%
93-A_S74_L001	5.1%	6.5%	93.2%	0.1%	91.0%	69.0	47.3%	99.7%	2.3%
94-A_S75_L001	3.8%	5.9%	93.7%	0.1%	93.3%	117.9	46.1%	99.5%	2.0%
95-A_S76_L001	1.7%	8.0%	91.8%	0.2%	91.3%	101.0	48.2%	99.3%	2.4%
96-A_S77_L001	4.3%	5.2%	94.5%	0.1%	90.7%	143.9	46.4%	99.4%	2.2%
97-A_S78_L001	0.8%	14.6%	83.9%	0.2%	91.5%	68.9	47.2%	99.2%	2.1%
98-A_S79_L001	2.6%	5.2%	92.5%	0.2%	91.2%	108.5	50.4%	99.4%	2.7%
99-A_S80_L001	0.9%	8.5%	91.1%	0.2%	91.9%	146.2	47.8%	99.5%	2.1%

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

Sort	Group	Column	Description	ID	Scale
\|\|	Kraken	% Blautia obeum	Percentage of reads that were the top Species over all samples - Blautia obeum	`% Blautia obeum`	None
\|\|	Kraken	% Top 5 Species	Percentage of reads that were classified by one of the top 5 Species (Blautia obeum, Akkermansia muciniphila, Prevotella copri, Bifidobacterium longum, Bacteroides fragilis)	`% Top 5`	None
\|\|	Kraken	% Unclassified	Percentage of reads that were unclassified	`% Unclassified`	None
\|\|	fastp	% Duplication	Duplication rate before filtering	`pct_duplication`	None
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`after_filtering_q30_rate`	None
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`after_filtering_q30_bases`	base_count
\|\|	fastp	GC content	GC content after filtering	`after_filtering_gc_content`	None
\|\|	fastp	% PF	Percent reads passing filter	`pct_surviving`	None
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`pct_adapter`	None

Software and Databases

Version of the programs used in the pipeline.

Showing ⁷/₇ rows.

Program	Version
cleanup/pipeline	v1.5
fastp	v0.23.2
seqfu	v1.14.0
kraken2	v2.1.0
pigz	v2.6
Host database	/qib/platforms/Informatics/transfer/outgoing/databases/kraken2/cleanup-db
Profiling database	/qib/platforms/Informatics/transfer/outgoing/databases/kraken2/gutcheck-db

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

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Version	Version	`Version`	None

Illumina indexes

Index data as found in the FASTQ files.

Showing ⁵⁰/₅₀ rows and ⁶/₆ columns.

Sample	PASS	Index	Ratio	Instrument	Run	Flowcell
80-A_S61_L001	PASS	61.0	1.00	M04971	n_87	000000000-CYT82
84-A_S65_L001	PASS	65.0	1.00	M04971	n_87	000000000-CYT82
2_S2_L001	PASS	2.0	1.00	M04971	n_83	000000000-CFLD9
75-A_S56_L001	PASS	56.0	1.00	M04971	n_87	000000000-CYT82
98-A_S79_L001	PASS	79.0	1.00	M04971	n_87	000000000-CYT82
112-A_S93_L001	PASS	93.0	1.00	M04971	n_87	000000000-CYT82
82-A_S63_L001	PASS	63.0	1.00	M04971	n_87	000000000-CYT82
100-A_S81_L001	PASS	81.0	1.00	M04971	n_87	000000000-CYT82
5_S5_L001	PASS	5.0	1.00	M04971	n_83	000000000-CFLD9
103-A_S84_L001	PASS	84.0	1.00	M04971	n_87	000000000-CYT82
89-A_S70_L001	PASS	70.0	1.00	M04971	n_87	000000000-CYT82
88-A_S69_L001	PASS	69.0	1.00	M04971	n_87	000000000-CYT82
86-A_S67_L001	PASS	67.0	1.00	M04971	n_87	000000000-CYT82
90-A_S71_L001	PASS	71.0	1.00	M04971	n_87	000000000-CYT82
69-A_S50_L001	PASS	50.0	1.00	M04971	n_87	000000000-CYT82
113-A_S94_L001	PASS	94.0	1.00	M04971	n_87	000000000-CYT82
73-A_S54_L001	PASS	54.0	1.00	M04971	n_87	000000000-CYT82
76-A_S57_L001	PASS	57.0	1.00	M04971	n_87	000000000-CYT82
4_S4_L001	PASS	4.0	1.00	M04971	n_83	000000000-CFLD9
87-A_S68_L001	PASS	68.0	1.00	M04971	n_87	000000000-CYT82
102-A_S83_L001	PASS	83.0	1.00	M04971	n_87	000000000-CYT82
92-A_S73_L001	PASS	73.0	1.00	M04971	n_87	000000000-CYT82
74-A_S55_L001	PASS	55.0	1.00	M04971	n_87	000000000-CYT82
93-A_S74_L001	PASS	74.0	1.00	M04971	n_87	000000000-CYT82
108-A_S89_L001	PASS	89.0	1.00	M04971	n_87	000000000-CYT82
97-A_S78_L001	PASS	78.0	1.00	M04971	n_87	000000000-CYT82
99-A_S80_L001	PASS	80.0	1.00	M04971	n_87	000000000-CYT82
78-A_S59_L001	PASS	59.0	1.00	M04971	n_87	000000000-CYT82
95-A_S76_L001	PASS	76.0	1.00	M04971	n_87	000000000-CYT82
3_S3_L001	PASS	3.0	1.00	M04971	n_83	000000000-CFLD9
81-A_S62_L001	PASS	62.0	1.00	M04971	n_87	000000000-CYT82
111-A_S92_L001	PASS	92.0	1.00	M04971	n_87	000000000-CYT82
101-A_S82_L001	PASS	82.0	1.00	M04971	n_87	000000000-CYT82
96-A_S77_L001	PASS	77.0	1.00	M04971	n_87	000000000-CYT82
109-A_S90_L001	PASS	90.0	1.00	M04971	n_87	000000000-CYT82
1_S1_L001	PASS	1.0	1.00	M04971	n_83	000000000-CFLD9
72-A_S53_L001	PASS	53.0	1.00	M04971	n_87	000000000-CYT82
106-A_S87_L001	PASS	87.0	1.00	M04971	n_87	000000000-CYT82
91-A_S72_L001	PASS	72.0	1.00	M04971	n_87	000000000-CYT82
79-A_S60_L001	PASS	60.0	1.00	M04971	n_87	000000000-CYT82
83-A_S64_L001	PASS	64.0	1.00	M04971	n_87	000000000-CYT82
104-A_S85_L001	PASS	85.0	1.00	M04971	n_87	000000000-CYT82
94-A_S75_L001	PASS	75.0	1.00	M04971	n_87	000000000-CYT82
77-A_S58_L001	PASS	58.0	1.00	M04971	n_87	000000000-CYT82
71-A_S52_L001	PASS	52.0	1.00	M04971	n_87	000000000-CYT82
107-A_S88_L001	PASS	88.0	1.00	M04971	n_87	000000000-CYT82
105-A_S86_L001	PASS	86.0	1.00	M04971	n_87	000000000-CYT82
70-A_S51_L001	PASS	51.0	1.00	M04971	n_87	000000000-CYT82
85-A_S66_L001	PASS	66.0	1.00	M04971	n_87	000000000-CYT82
110-A_S91_L001	PASS	91.0	1.00	M04971	n_87	000000000-CYT82

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

Sort	Group	Column	Description	ID	Scale
\|\|	Cust Data	PASS	Enough reads have the same index	`col3`	None
\|\|	Cust Data	Index	Detected Illumina index	`col1`	None
\|\|	Cust Data	Ratio	Ratio of reads with the most common index on the total	`col2`	None
\|\|	Cust Data	Instrument	Intrument ID	`col4`	None
\|\|	Cust Data	Run	Run	`col5`	None
\|\|	Cust Data	Flowcell	Ratio of large chromosomes/total human chromosomes	`col6`	None

Host removal

Summary host removal and read filtering step.

Showing ⁵⁰/₅₀ rows and ⁷/₇ columns.

Sample	Raw sequences	Host (%)	Non-host reads	PF (%)	Cleaned reads	Contaminants reads	HG-Check
100-A_S81_L001	195552	0.01%	195532	99.60%	194774	N/A	No chr contam
101-A_S82_L001	212472	0.16%	212127	99.11%	210575	N/A	0.3
102-A_S83_L001	289611	0.01%	289590	99.27%	287504	N/A	No chr contam
103-A_S84_L001	125281	0.02%	125254	99.15%	124212	N/A	No chr contam
104-A_S85_L001	100117	0.26%	99859	93.41%	93521	N/A	0.2
105-A_S86_L001	380606	0.01%	380560	99.22%	377627	N/A	No chr contam
106-A_S87_L001	101671	0.01%	101657	99.50%	101165	N/A	No chr contam
107-A_S88_L001	444924	0.07%	444615	99.45%	442485	N/A	1.0
108-A_S89_L001	50876	0.07%	50842	98.31%	50014	N/A	0.6
109-A_S90_L001	226527	0.04%	226435	99.29%	224918	N/A	No chr contam
110-A_S91_L001	457002	0.98%	452507	98.52%	450250	N/A	0.3
111-A_S92_L001	360429	0.01%	360378	99.47%	358501	N/A	No chr contam
112-A_S93_L001	258630	0.18%	258167	99.23%	256643	N/A	0.3
113-A_S94_L001	89511	0.38%	89171	97.55%	87314	N/A	0.3
1_S1_L001	1217977	0.05%	1217372	99.38%	1210391	N/A	No chr contam
2_S2_L001	239265	0.11%	238998	98.66%	236065	N/A	0.4
3_S3_L001	339260	0.03%	339146	98.48%	334116	N/A	No chr contam
4_S4_L001	391444	0.07%	391188	99.28%	388614	N/A	1.0
5_S5_L001	663364	0.03%	663141	99.28%	658615	N/A	No chr contam
69-A_S50_L001	114079	0.02%	114055	99.74%	113785	N/A	No chr contam
70-A_S51_L001	193979	0.03%	193923	99.75%	193485	N/A	No chr contam
71-A_S52_L001	163092	0.07%	162980	99.68%	162572	N/A	0.7
72-A_S53_L001	143869	0.02%	143842	99.66%	143374	N/A	No chr contam
73-A_S54_L001	278729	0.42%	277561	99.14%	276322	N/A	0.3
74-A_S55_L001	258621	0.03%	258554	99.64%	257683	N/A	No chr contam
75-A_S56_L001	322690	0.07%	322452	99.27%	320326	N/A	0.7
76-A_S57_L001	48008	0.04%	47988	99.73%	47876	N/A	0.0
77-A_S58_L001	119412	0.02%	119386	99.32%	118595	N/A	No chr contam
78-A_S59_L001	416384	0.02%	416292	99.44%	414058	N/A	No chr contam
79-A_S60_L001	186443	0.04%	186366	99.49%	185492	N/A	No chr contam
80-A_S61_L001	144673	0.02%	144638	99.67%	144199	N/A	No chr contam
81-A_S62_L001	129643	0.02%	129612	99.50%	128997	N/A	No chr contam
82-A_S63_L001	366292	0.01%	366261	99.44%	364244	N/A	No chr contam
83-A_S64_L001	244273	0.00%	244267	99.75%	243666	N/A	No chr contam
84-A_S65_L001	91265	0.04%	91229	99.27%	90599	N/A	No chr contam
85-A_S66_L001	338996	0.01%	338975	99.44%	337107	N/A	No chr contam
86-A_S67_L001	112664	0.02%	112645	99.20%	111761	N/A	No chr contam
87-A_S68_L001	327087	0.01%	327039	99.40%	325126	N/A	No chr contam
88-A_S69_L001	244588	0.13%	244274	99.30%	242877	N/A	0.6
89-A_S70_L001	292647	0.04%	292530	99.63%	291566	N/A	No chr contam
90-A_S71_L001	410228	0.04%	410075	99.48%	408089	N/A	No chr contam
91-A_S72_L001	471664	0.01%	471627	99.56%	469586	N/A	No chr contam
92-A_S73_L001	383993	0.01%	383960	99.45%	381875	N/A	No chr contam
93-A_S74_L001	148865	0.01%	148843	99.70%	148412	N/A	No chr contam
94-A_S75_L001	275287	0.01%	275259	99.46%	273813	N/A	No chr contam
95-A_S76_L001	223647	0.02%	223607	99.26%	221982	N/A	No chr contam
96-A_S77_L001	325514	0.01%	325486	99.44%	323693	N/A	No chr contam
97-A_S78_L001	151517	0.03%	151473	99.14%	150217	N/A	No chr contam
98-A_S79_L001	239488	0.12%	239190	99.23%	237648	N/A	0.4
99-A_S80_L001	328431	0.08%	328175	99.43%	326549	N/A	1.0

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

Sort	Group	Column	Description	ID	Scale
\|\|	Cust Data	Raw sequences	Initial number of sequences	`col1`	None
\|\|	Cust Data	Host (%)	Fraction of host reads	`col2`	None
\|\|	Cust Data	Non-host reads	Number of reads after host removal	`col3`	None
\|\|	Cust Data	PF (%)	Fraction of reads passing filters (host removal and adapter trimming)	`col4`	None
\|\|	Cust Data	Cleaned reads	Number of reads after fastp filter	`col5`	None
\|\|	Cust Data	Contaminants reads	Number of contaminants reads (optional step)	`col6`	None
\|\|	Cust Data	HG-Check	Ratio of large chromosomes/total human chromosomes	`col7`	None

Kraken

Kraken is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.DOI: 10.1186/gb-2014-15-3-r46.

Top taxa

The number of reads falling into the top 5 taxa across different ranks.

To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top five taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

fastp

fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).DOI: 10.1093/bioinformatics/bty560.

Filtered Reads

Filtering statistics of sampled reads.

Insert Sizes

Insert size estimation of sampled reads.

Sequence Quality

Average sequencing quality over each base of all reads.

GC Content

Average GC content over each base of all reads.

N content

Average N content over each base of all reads.

Toggle navigation v1.13.dev0

GMH/cleanup

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

GMH/cleanup A prescreening pipeline for GMH Metagenome studies

General Statistics

General Statistics: Columns

Software and Databases

Versions-Plot: Columns

Illumina indexes

Index-Plot: Columns

Host removal

Summary-Plot: Columns

Kraken

Top taxa Help

fastp

Filtered Reads

Insert Sizes

Sequence Quality

GC Content

N content

v1.13.dev0

Highlight Samples

Rename Samples

Show / Hide Samples

GMH/cleanup
A prescreening pipeline for GMH Metagenome studies

Top taxa