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

Report generated on 2025-01-20, 18:10 based on data in:
/scratch/sysuser/jonathan/nicd_admin/20250116_AV242303_Dineo_E_coli_B1/assemblyMetrics/quast

General Statistics

Sample NameM Reads MappedN50 (Kbp)Length (Mbp)
Control-03
139.6Kbp
5.2Mbp
Control_03.stat
1.5
ROB-CVLBACT2301
1.5Kbp
5.1Mbp
ROB-CVLBACT2302
2.5Kbp
5.5Mbp
ROB-CVLBACT2303
4.7Kbp
5.2Mbp
ROB-CVLBACT2304
2.5Kbp
5.8Mbp
ROB-CVLBACT2305
61.5Kbp
10.4Mbp
ROB-CVLBACT2306
86.5Kbp
4.7Mbp
ROB-CVLBACT2307
4.3Kbp
6.4Mbp
ROB-CVLBACT2308
115.3Kbp
4.7Mbp
ROB-CVLBACT2309
273.4Kbp
5.2Mbp
ROB-CVLBACT2310
502.4Kbp
5.9Mbp
ROB-CVLBACT2411
1.3Kbp
13.8Mbp
ROB_CVLBACT2301.stat
1.8
ROB_CVLBACT2302.stat
4.0
ROB_CVLBACT2303.stat
5.1
ROB_CVLBACT2304.stat
5.4
ROB_CVLBACT2305.stat
6.2
ROB_CVLBACT2306.stat
7.2
ROB_CVLBACT2307.stat
5.8
ROB_CVLBACT2308.stat
2.5
ROB_CVLBACT2309.stat
3.3
ROB_CVLBACT2310.stat
3.8
ROB_CVLBACT2411.stat
2.8

QUAST

QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

Assembly Statistics

Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)
Control-03
139.6Kbp
63.1Kbp
0.0K
26.0K
440.7Kbp
5.2Mbp
ROB-CVLBACT2301
1.5Kbp
0.8Kbp
0.8K
1983.0K
33.0Kbp
5.1Mbp
ROB-CVLBACT2302
2.5Kbp
1.3Kbp
0.6K
1324.0K
48.2Kbp
5.5Mbp
ROB-CVLBACT2303
4.7Kbp
2.0Kbp
0.3K
728.0K
38.4Kbp
5.2Mbp
ROB-CVLBACT2304
2.5Kbp
1.3Kbp
0.6K
1429.0K
29.7Kbp
5.8Mbp
ROB-CVLBACT2305
61.5Kbp
21.5Kbp
0.0K
113.0K
443.0Kbp
10.4Mbp
ROB-CVLBACT2306
86.5Kbp
45.0Kbp
0.0K
35.0K
304.5Kbp
4.7Mbp
ROB-CVLBACT2307
4.3Kbp
1.9Kbp
0.4K
951.0K
85.9Kbp
6.4Mbp
ROB-CVLBACT2308
115.3Kbp
77.9Kbp
0.0K
24.0K
342.7Kbp
4.7Mbp
ROB-CVLBACT2309
273.4Kbp
165.8Kbp
0.0K
11.0K
763.0Kbp
5.2Mbp
ROB-CVLBACT2310
502.4Kbp
235.6Kbp
0.0K
8.0K
1292.2Kbp
5.9Mbp
ROB-CVLBACT2411
1.3Kbp
0.7Kbp
1.9K
5745.0K
86.7Kbp
13.8Mbp

Number of Contigs

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

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools Flagstat

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

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