A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2017-11-15, 21:47 based on data in:
/buffer/ag_abi/kneubert/brucella_assembly_refs/fastqc
/buffer/ag_abi/kneubert/brucella_assembly_refs/fastq_screen
/buffer/ag_abi/kneubert/brucella_assembly_refs/mini_kraken_summary
General Statistics
Showing 176/176 rows and 4/5 columns.Sample Name | % Dups | % GC | Length | M Seqs |
---|---|---|---|---|
ES-0001a_1 | 16.6% | 56% | 284 bp | 0.5 |
ES-0001a_2 | 15.7% | 57% | 285 bp | 0.5 |
ES-0001b_1 | 27.5% | 57% | 254 bp | 1.2 |
ES-0001b_2 | 25.9% | 57% | 258 bp | 1.2 |
ES-0001c_1 | 22.5% | 57% | 278 bp | 0.8 |
ES-0001c_2 | 18.2% | 59% | 280 bp | 0.8 |
ES-0002a_1 | 20.7% | 56% | 241 bp | 0.7 |
ES-0002a_2 | 20.1% | 56% | 242 bp | 0.7 |
ES-0002b_1 | 23.8% | 57% | 253 bp | 0.9 |
ES-0002b_2 | 22.3% | 57% | 260 bp | 0.9 |
ES-0002c_1 | 15.8% | 57% | 281 bp | 0.5 |
ES-0002c_2 | 13.4% | 57% | 282 bp | 0.5 |
ES-0003a_1 | 10.8% | 57% | 283 bp | 0.3 |
ES-0003a_2 | 10.2% | 57% | 283 bp | 0.3 |
ES-0003b_1 | 24.1% | 57% | 266 bp | 1.0 |
ES-0003b_2 | 22.6% | 57% | 270 bp | 1.0 |
ES-0003c_1 | 31.1% | 57% | 266 bp | 1.4 |
ES-0003c_2 | 29.4% | 57% | 268 bp | 1.4 |
ES-0004a_1 | 8.6% | 56% | 263 bp | 0.2 |
ES-0004a_2 | 8.2% | 56% | 264 bp | 0.2 |
ES-0004b_1 | 23.5% | 57% | 263 bp | 0.9 |
ES-0004b_2 | 22.2% | 57% | 267 bp | 0.9 |
ES-0004c_1 | 22.4% | 57% | 276 bp | 0.9 |
ES-0004c_2 | 20.4% | 57% | 276 bp | 0.9 |
ES-0005a_1 | 15.8% | 56% | 250 bp | 0.5 |
ES-0005a_2 | 15.1% | 56% | 251 bp | 0.5 |
ES-0005b_1 | 23.1% | 57% | 271 bp | 0.9 |
ES-0005b_2 | 21.6% | 57% | 273 bp | 0.9 |
ES-0005c_1 | 20.8% | 57% | 279 bp | 0.8 |
ES-0005c_2 | 18.8% | 57% | 280 bp | 0.8 |
ES-0006a_1 | 26.6% | 57% | 262 bp | 1.1 |
ES-0006a_2 | 24.4% | 57% | 266 bp | 1.1 |
ES-0006b_1 | 25.3% | 57% | 256 bp | 1.0 |
ES-0006b_2 | 23.8% | 57% | 260 bp | 1.0 |
ES-0006c_1 | 24.7% | 57% | 268 bp | 1.0 |
ES-0006c_2 | 23.5% | 57% | 269 bp | 1.0 |
ES-0007a_1 | 11.9% | 57% | 279 bp | 0.3 |
ES-0007a_2 | 11.0% | 57% | 280 bp | 0.3 |
ES-0007b_1 | 31.4% | 57% | 238 bp | 1.4 |
ES-0007b_2 | 30.1% | 57% | 242 bp | 1.4 |
ES-0007c_1 | 24.4% | 57% | 273 bp | 0.9 |
ES-0007c_2 | 19.8% | 59% | 278 bp | 0.9 |
ES-0008a_1 | 17.6% | 56% | 281 bp | 0.6 |
ES-0008a_2 | 16.7% | 57% | 282 bp | 0.6 |
ES-0008b_1 | 18.0% | 57% | 275 bp | 0.6 |
ES-0008b_2 | 16.7% | 57% | 277 bp | 0.6 |
ES-0008c_1 | 29.0% | 57% | 264 bp | 1.3 |
ES-0008c_2 | 27.4% | 57% | 266 bp | 1.3 |
ES-0009a_1 | 16.8% | 56% | 277 bp | 0.5 |
ES-0009a_2 | 16.2% | 57% | 278 bp | 0.5 |
ES-0009b_1 | 24.4% | 57% | 250 bp | 1.0 |
ES-0009b_2 | 23.1% | 57% | 254 bp | 1.0 |
ES-0009c_1 | 17.8% | 57% | 258 bp | 0.6 |
ES-0009c_2 | 15.1% | 59% | 261 bp | 0.6 |
ES-0010a_1 | 18.9% | 56% | 276 bp | 0.6 |
ES-0010a_2 | 18.1% | 57% | 277 bp | 0.6 |
ES-0010b_1 | 23.6% | 57% | 269 bp | 0.9 |
ES-0010b_2 | 21.9% | 57% | 272 bp | 0.9 |
ES-0010c_1 | 15.1% | 57% | 274 bp | 0.5 |
ES-0010c_2 | 11.4% | 59% | 277 bp | 0.5 |
ES-0011a_1 | 18.2% | 56% | 288 bp | 0.6 |
ES-0011a_2 | 17.4% | 57% | 288 bp | 0.6 |
ES-0011b_1 | 20.2% | 57% | 281 bp | 0.7 |
ES-0011b_2 | 18.1% | 57% | 282 bp | 0.7 |
ES-0011c_1 | 12.7% | 56% | 265 bp | 0.2 |
ES-0011c_2 | 10.4% | 58% | 270 bp | 0.2 |
ES-0012a_1 | 11.7% | 56% | 291 bp | 0.3 |
ES-0012a_2 | 10.8% | 57% | 292 bp | 0.3 |
ES-0012b_1 | 18.5% | 57% | 273 bp | 0.6 |
ES-0012b_2 | 16.9% | 57% | 275 bp | 0.6 |
ES-0012c_1 | 30.1% | 57% | 235 bp | 1.4 |
ES-0012c_2 | 28.8% | 57% | 238 bp | 1.4 |
ES-0013a_1 | 21.8% | 57% | 274 bp | 0.8 |
ES-0013a_2 | 19.8% | 57% | 276 bp | 0.8 |
ES-0013b_1 | 22.8% | 57% | 268 bp | 0.8 |
ES-0013b_2 | 20.9% | 57% | 271 bp | 0.8 |
ES-0013c_1 | 20.9% | 57% | 274 bp | 0.7 |
ES-0013c_2 | 17.1% | 59% | 280 bp | 0.7 |
ES-0014a_1 | 13.8% | 56% | 254 bp | 0.4 |
ES-0014a_2 | 13.1% | 56% | 255 bp | 0.4 |
ES-0014b_1 | 21.7% | 57% | 251 bp | 0.8 |
ES-0014b_2 | 20.6% | 57% | 255 bp | 0.8 |
ES-0014c_1 | 17.0% | 57% | 283 bp | 0.6 |
ES-0014c_2 | 14.5% | 57% | 284 bp | 0.6 |
ES-0015a_1 | 23.2% | 56% | 249 bp | 0.9 |
ES-0015a_2 | 22.7% | 56% | 250 bp | 0.9 |
ES-0015b_1 | 25.8% | 57% | 261 bp | 1.1 |
ES-0015b_2 | 24.6% | 57% | 264 bp | 1.1 |
ES-0015c_1 | 16.9% | 57% | 276 bp | 0.5 |
ES-0015c_2 | 12.0% | 59% | 279 bp | 0.5 |
ES-0016a_1 | 13.9% | 56% | 265 bp | 0.4 |
ES-0016a_2 | 13.2% | 57% | 266 bp | 0.4 |
ES-0016b_1 | 23.4% | 56% | 243 bp | 0.9 |
ES-0016b_2 | 22.3% | 57% | 246 bp | 0.9 |
ES-0016c_1 | 23.8% | 57% | 264 bp | 0.9 |
ES-0016c_2 | 22.4% | 57% | 265 bp | 0.9 |
ES-0017a_1 | 16.2% | 56% | 256 bp | 0.5 |
ES-0017a_2 | 15.5% | 56% | 257 bp | 0.5 |
ES-0017b_1 | 19.3% | 57% | 282 bp | 0.7 |
ES-0017b_2 | 17.5% | 57% | 283 bp | 0.7 |
ES-0017c_1 | 14.5% | 57% | 265 bp | 0.4 |
ES-0017c_2 | 10.7% | 59% | 270 bp | 0.4 |
ES-0018a_1 | 15.8% | 56% | 245 bp | 0.5 |
ES-0018a_2 | 15.2% | 56% | 246 bp | 0.5 |
ES-0018b_1 | 19.6% | 56% | 259 bp | 0.7 |
ES-0018b_2 | 18.1% | 56% | 262 bp | 0.7 |
ES-0018c_1 | 16.6% | 56% | 273 bp | 0.6 |
ES-0018c_2 | 14.9% | 57% | 274 bp | 0.6 |
ES-0019a_1 | 1.8% | 56% | 288 bp | 0.0 |
ES-0019a_2 | 1.8% | 57% | 288 bp | 0.0 |
ES-0019b_1 | 18.5% | 57% | 269 bp | 0.7 |
ES-0019b_2 | 16.8% | 57% | 270 bp | 0.7 |
ES-0019c_1 | 24.2% | 56% | 231 bp | 1.1 |
ES-0019c_2 | 23.7% | 57% | 234 bp | 1.1 |
ES-0020a_1 | 27.2% | 57% | 263 bp | 1.1 |
ES-0020a_2 | 25.6% | 57% | 267 bp | 1.1 |
ES-0020b_1 | 26.0% | 57% | 246 bp | 1.0 |
ES-0020b_2 | 24.9% | 57% | 249 bp | 1.0 |
ES-0020c_1 | 25.2% | 57% | 273 bp | 1.0 |
ES-0020c_2 | 23.3% | 57% | 274 bp | 1.0 |
ES-0021a_1 | 14.7% | 56% | 277 bp | 0.4 |
ES-0021a_2 | 14.0% | 57% | 277 bp | 0.4 |
ES-0021b_1 | 26.0% | 57% | 261 bp | 1.0 |
ES-0021b_2 | 24.4% | 57% | 264 bp | 1.0 |
ES-0021c_1 | 18.0% | 57% | 284 bp | 0.6 |
ES-0021c_2 | 15.9% | 57% | 285 bp | 0.6 |
ES-0022a_1 | 15.8% | 56% | 270 bp | 0.5 |
ES-0022a_2 | 15.2% | 56% | 271 bp | 0.5 |
ES-0022b_1 | 22.5% | 57% | 272 bp | 0.8 |
ES-0022b_2 | 20.6% | 57% | 274 bp | 0.8 |
ES-0022c_1 | 15.8% | 57% | 259 bp | 0.6 |
ES-0022c_2 | 13.8% | 57% | 259 bp | 0.6 |
ES-0023a_1 | 17.7% | 56% | 272 bp | 0.6 |
ES-0023a_2 | 17.2% | 56% | 273 bp | 0.6 |
ES-0023b_1 | 11.7% | 56% | 269 bp | 0.2 |
ES-0023b_2 | 10.9% | 56% | 270 bp | 0.2 |
ES-0023c_1 | 10.7% | 57% | 256 bp | 0.4 |
ES-0023c_2 | 9.0% | 57% | 257 bp | 0.4 |
ES-0024a_1 | 11.5% | 56% | 274 bp | 0.3 |
ES-0024a_2 | 11.2% | 57% | 275 bp | 0.3 |
ES-0024b_1 | 6.2% | 57% | 283 bp | 0.1 |
ES-0024b_2 | 5.7% | 57% | 284 bp | 0.1 |
ES-0024c_1 | 21.3% | 57% | 275 bp | 0.8 |
ES-0024c_2 | 18.6% | 57% | 276 bp | 0.8 |
ES-0025a_1 | 15.5% | 56% | 254 bp | 0.5 |
ES-0025a_2 | 15.0% | 56% | 254 bp | 0.5 |
ES-0025b_1 | 15.0% | 56% | 280 bp | 0.5 |
ES-0025b_2 | 14.4% | 57% | 281 bp | 0.5 |
ES-0025c_1 | 18.9% | 57% | 274 bp | 0.6 |
ES-0025c_2 | 14.0% | 59% | 280 bp | 0.6 |
ES-0026a_1 | 12.4% | 56% | 272 bp | 0.4 |
ES-0026a_2 | 11.8% | 56% | 273 bp | 0.4 |
ES-0026b_1 | 12.3% | 56% | 258 bp | 0.4 |
ES-0026b_2 | 11.9% | 57% | 259 bp | 0.4 |
ES-0026c_1 | 22.6% | 57% | 271 bp | 0.9 |
ES-0026c_2 | 20.5% | 57% | 271 bp | 0.9 |
ES-0027b_1 | 12.9% | 56% | 283 bp | 0.3 |
ES-0027b_2 | 12.0% | 57% | 284 bp | 0.3 |
ES-0027c_1 | 33.5% | 57% | 238 bp | 1.5 |
ES-0027c_2 | 32.8% | 57% | 240 bp | 1.5 |
ES-0028a_1 | 16.2% | 56% | 262 bp | 0.5 |
ES-0028a_2 | 15.8% | 56% | 263 bp | 0.5 |
ES-0028b_1 | 13.3% | 56% | 272 bp | 0.4 |
ES-0028b_2 | 12.5% | 57% | 273 bp | 0.4 |
ES-0028c_1 | 17.0% | 57% | 273 bp | 0.6 |
ES-0028c_2 | 12.4% | 59% | 278 bp | 0.6 |
ES-0132a_1 | 16.8% | 57% | 261 bp | 0.6 |
ES-0132a_2 | 16.2% | 57% | 265 bp | 0.6 |
ES-0132b_1 | 21.3% | 57% | 277 bp | 0.8 |
ES-0132b_2 | 19.3% | 58% | 278 bp | 0.8 |
ES-0133a_1 | 19.8% | 57% | 282 bp | 0.7 |
ES-0133a_2 | 17.7% | 58% | 283 bp | 0.7 |
ES-0133b_1 | 25.2% | 57% | 273 bp | 0.8 |
ES-0133b_2 | 22.8% | 57% | 275 bp | 0.8 |
ES-0133c_1 | 12.4% | 57% | 283 bp | 0.4 |
ES-0133c_2 | 10.7% | 58% | 284 bp | 0.4 |
Kraken Genus Map Report
Kraken Genus Map Report kraken-mpa-report --db $minikrakenDB mini_kraken/*sequences.kraken >mini_kraken/mpa_report.tsv
Kraken Species Map Report
Kraken Species Map Report kraken-mpa-report --db /group/ag_abi/kneubert/soft/Kraken/krakenDB/minikraken_20171019_8GB mini_kraken/*sequences.kraken >mini_kraken/mpa_report.tsv
FastQ Screen
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
FastQC
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
Sequence Quality Histograms
The mean quality value across each base position in the read. See the FastQC help.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Per Base N Content
The percentage of base calls at each position for which an N was called. See the FastQC help.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Sequence Length Distribution
The distribution of fragment sizes (read lengths) found. See the FastQC help.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Sequence Duplication Levels
The relative level of duplication found for every sequence. See the FastQC help.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Overrepresented sequences
The total amount of overrepresented sequences found in each library. See the FastQC help for further information.
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).