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 Name | M Reads Mapped | N50 (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 Name | N50 (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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