# HG changeset patch # User iuc # Date 1538177429 14400 # Node ID db1eeffba23e9bfe3b088f1df2ee415a62d2bb19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 diff -r 000000000000 -r db1eeffba23e nanoplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nanoplot.xml Fri Sep 28 19:30:29 2018 -0400 @@ -0,0 +1,468 @@ + + Plotting suite for Oxford Nanopore sequencing data and alignments + + nanoplot + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + @misc{githubnanoplot, author = {De Coster, Wouter}, year = {2018}, title = + {NanoPlot}, publisher = {GitHub}, journal = {GitHub repository}, url = + {https://github.com/wdecoster/NanoPlot}, } + 10.1093/bioinformatics/bty149 + +
diff -r 000000000000 -r db1eeffba23e test-data/HistogramReadlength.jpg Binary file test-data/HistogramReadlength.jpg has changed diff -r 000000000000 -r db1eeffba23e test-data/NanoPlot-report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NanoPlot-report.html Fri Sep 28 19:30:29 2018 -0400 @@ -0,0 +1,362 @@ + + + + + + NanoPlot Report + +
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Summary Statistics prior to filtering

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Summary Statistics after filtering

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Plots

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Histogram of read lengths

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Histogram of read lengths after log transformation

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Weighted Histogram of read lengths

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Weighted Histogram of read lengths after log transformation

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Yield by length

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Read lengths vs Average read quality plot using hexagonal bins

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Read lengths vs Average read quality plot using a kernel density estimation

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Number of reads generated per channel

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Cumulative yield

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Cumulative yield

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Number of reads over time

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Number of active pores over time

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Violin plot of read lengths over time

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Violin plot of quality over time

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NanoPlot report

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Summary statistics prior to filtering

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General summary:
Active channels:169
Mean read length:23212.6
Mean read quality:10.1
Median read length:9390.0
Median read quality:10.3
Number of reads:371
Read length N50:60395
Total bases:8611871
Number, percentage and megabases of reads above quality cutoffs
>Q5:371 (100.0%) 8.6Mb
>Q7:371 (100.0%) 8.6Mb
>Q10:207 (55.8%) 4.7Mb
>Q12:49 (13.2%) 0.9Mb
>Q15:0 (0.0%) 0.0Mb
Top 5 highest mean basecall quality scores and their read lengths
1:13.3 (6333)
2:13.1 (5448)
3:12.9 (27834)
4:12.8 (20351)
5:12.8 (97730)
Top 5 longest reads and their mean basecall quality score
1:393431 (10.6)
2:341725 (11.8)
3:320662 (8.0)
4:226843 (9.1)
5:221901 (10.0)
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Summary statistics after filtering

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General summary:
Active channels:169
Mean read length:23212.6
Mean read quality:10.1
Median read length:9390.0
Median read quality:10.3
Number of reads:371
Read length N50:60395
Total bases:8611871
Number, percentage and megabases of reads above quality cutoffs
>Q5:371 (100.0%) 8.6Mb
>Q7:371 (100.0%) 8.6Mb
>Q10:207 (55.8%) 4.7Mb
>Q12:49 (13.2%) 0.9Mb
>Q15:0 (0.0%) 0.0Mb
Top 5 highest mean basecall quality scores and their read lengths
1:13.3 (6333)
2:13.1 (5448)
3:12.9 (27834)
4:12.8 (20351)
5:12.8 (97730)
Top 5 longest reads and their mean basecall quality score
1:393431 (10.6)
2:341725 (11.8)
3:320662 (8.0)
4:226843 (9.1)
5:221901 (10.0)
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Plots

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Histogram of read lengths

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Histogram of read lengths after log transformation

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Weighted Histogram of read lengths

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Weighted Histogram of read lengths after log transformation

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Yield by length

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Read lengths vs Average read quality plot using hexagonal bins

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Read lengths vs Average read quality plot using a kernel density estimation

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Number of reads generated per channel

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Cumulative yield

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Cumulative yield

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Number of reads over time

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Number of active pores over time

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Violin plot of read lengths over time

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Violin plot of quality over time

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\ No newline at end of file diff -r 000000000000 -r db1eeffba23e test-data/NanoStats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NanoStats.txt Fri Sep 28 19:30:29 2018 -0400 @@ -0,0 +1,27 @@ +General summary: +Active channels: 169 +Mean read length: 23212.6 +Mean read quality: 10.1 +Median read length: 9390.0 +Median read quality: 10.3 +Number of reads: 371 +Read length N50: 60395 +Total bases: 8611871 +Number, percentage and megabases of reads above quality cutoffs +>Q5: 371 (100.0%) 8.6Mb +>Q7: 371 (100.0%) 8.6Mb +>Q10: 207 (55.8%) 4.7Mb +>Q12: 49 (13.2%) 0.9Mb +>Q15: 0 (0.0%) 0.0Mb +Top 5 highest mean basecall quality scores and their read lengths +1: 13.3 (6333) +2: 13.1 (5448) +3: 12.9 (27834) +4: 12.8 (20351) +5: 12.8 (97730) +Top 5 longest reads and their mean basecall quality score +1: 393431 (10.6) +2: 341725 (11.8) +3: 320662 (8.0) +4: 226843 (9.1) +5: 221901 (10.0) diff -r 000000000000 -r db1eeffba23e test-data/NanoStats_post_filtering.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NanoStats_post_filtering.txt Fri Sep 28 19:30:29 2018 -0400 @@ -0,0 +1,27 @@ +General summary: +Active channels: 169 +Mean read length: 23212.6 +Mean read quality: 10.1 +Median read length: 9390.0 +Median read quality: 10.3 +Number of reads: 371 +Read length N50: 60395 +Total bases: 8611871 +Number, percentage and megabases of reads above quality cutoffs +>Q5: 371 (100.0%) 8.6Mb +>Q7: 371 (100.0%) 8.6Mb +>Q10: 207 (55.8%) 4.7Mb +>Q12: 49 (13.2%) 0.9Mb +>Q15: 0 (0.0%) 0.0Mb +Top 5 highest mean basecall quality scores and their read lengths +1: 13.3 (6333) +2: 13.1 (5448) +3: 12.9 (27834) +4: 12.8 (20351) +5: 12.8 (97730) +Top 5 longest reads and their mean basecall quality score +1: 393431 (10.6) +2: 341725 (11.8) +3: 320662 (8.0) +4: 226843 (9.1) +5: 221901 (10.0) diff -r 000000000000 -r db1eeffba23e test-data/alignment.bam Binary file test-data/alignment.bam has changed diff -r 000000000000 -r db1eeffba23e test-data/bam-LogTransformed_HistogramReadlength.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam-LogTransformed_HistogramReadlength.svg Fri Sep 28 19:30:29 2018 -0400 @@ -0,0 +1,927 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r db1eeffba23e test-data/bam-report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam-report.html Fri Sep 28 19:30:29 2018 -0400 @@ -0,0 +1,401 @@ + + + + + + NanoPlot Report + +
+

Summary Statistics prior to filtering

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Summary Statistics after filtering

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Plots

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Histogram of read lengths

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Histogram of read lengths after log transformation

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Weighted Histogram of read lengths

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Weighted Histogram of read lengths after log transformation

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Yield by length

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Read lengths vs Average read quality plot using dots

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Read lengths vs Average read quality plot using a kernel density estimation

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Aligned read lengths vs Sequenced read length plot using dots

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Aligned read lengths vs Sequenced read length plot using a kernel density estimation

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Read mapping quality vs Average basecall quality plot using dots

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Read mapping quality vs Average basecall quality plot using a kernel density estimation

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Read length vs Read mapping quality plot using dots

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Read length vs Read mapping quality plot using a kernel density estimation

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Percent identity vs Average Base Quality plot using dots

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Percent identity vs Average Base Quality plot using a kernel density estimation

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Aligned read length vs Percent identity plot using dots

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Aligned read length vs Percent identity plot using a kernel density estimation

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NanoPlot report

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Summary statistics prior to filtering

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General summary:
Average percent identity:85.3
Mean read length:12291.0
Mean read quality:13.2
Median percent identity:87.3
Median read length:7577.0
Median read quality:13.5
Number of reads:1115
Read length N50:21987
Total bases:13704509
Total bases aligned:12343518
Number, percentage and megabases of reads above quality cutoffs
>Q5:1115 (100.0%) 13.7Mb
>Q7:1115 (100.0%) 13.7Mb
>Q10:1098 (98.5%) 13.6Mb
>Q12:936 (83.9%) 11.9Mb
>Q15:10 (0.9%) 0.0Mb
Top 5 highest mean basecall quality scores and their read lengths
1:15.7 (1461; SRR5665597.758)
2:15.5 (1790; SRR5665597.725)
3:15.5 (615; SRR5665597.293)
4:15.5 (162; SRR5665597.876)
5:15.5 (626; SRR5665597.822)
Top 5 longest reads and their mean basecall quality score
1:99139 (13.9; SRR5665597.31)
2:80522 (13.5; SRR5665597.790)
3:79569 (13.5; SRR5665597.332)
4:70195 (10.2; SRR5665597.799)
5:69426 (12.2; SRR5665597.1000)
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Summary statistics after filtering

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General summary:
Average percent identity:85.0
Mean read length:1436.3
Mean read quality:13.1
Median percent identity:86.8
Median read length:1419.5
Median read quality:13.4
Number of reads:80
Read length N50:1474
Total bases:114904
Total bases aligned:110215
Number, percentage and megabases of reads above quality cutoffs
>Q5:80 (100.0%) 0.1Mb
>Q7:80 (100.0%) 0.1Mb
>Q10:77 (96.2%) 0.1Mb
>Q12:64 (80.0%) 0.1Mb
>Q15:3 (3.8%) 0.0Mb
Top 5 highest mean basecall quality scores and their read lengths
1:15.7 (1461; SRR5665597.758)
2:15.5 (1790; SRR5665597.725)
3:15.1 (1474; SRR5665597.822)
4:14.7 (1985; SRR5665597.268)
5:14.6 (1726; SRR5665597.119)
Top 5 longest reads and their mean basecall quality score
1:1985 (14.7; SRR5665597.268)
2:1981 (13.2; SRR5665597.912)
3:1969 (13.2; SRR5665597.827)
4:1955 (13.2; SRR5665597.213)
5:1930 (11.1; SRR5665597.21)
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Plots

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Histogram of read lengths

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Histogram of read lengths after log transformation

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Weighted Histogram of read lengths

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Weighted Histogram of read lengths after log transformation

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Yield by length

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Read lengths vs Average read quality plot using dots

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Read lengths vs Average read quality plot using a kernel density estimation

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Aligned read lengths vs Sequenced read length plot using dots

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Aligned read lengths vs Sequenced read length plot using a kernel density estimation

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Read mapping quality vs Average basecall quality plot using dots

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Read mapping quality vs Average basecall quality plot using a kernel density estimation

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Read length vs Read mapping quality plot using dots

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Read length vs Read mapping quality plot using a kernel density estimation

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Percent identity vs Average Base Quality plot using dots

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Percent identity vs Average Base Quality plot using a kernel density estimation

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Aligned read length vs Percent identity plot using dots

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Aligned read length vs Percent identity plot using a kernel density estimation

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