jvarkit
FastqEntropy
Compute the Entropy of a Fastq file (distribution of the length(gzipped(sequence))
Usage
Usage: fastqentropy [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
Keywords
- fastq
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew fastqentropy
The java jar file will be installed in the dist directory.
Source code
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite fastqentropy ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Example
$ java -jar dist/fastqentropy.jar file.fastq.gz
output (length/count):
36 1
37 1
38 2
39 2
128 3
41 7
40 9
127 10
42 18
43 20
44 34
126 35
45 71
46 114
125 114
47 198
124 254
48 272
49 475
123 552
50 579
51 787
52 1028
122 1085
53 1281
54 1391
55 1624
121 1846
56 1847
57 1907
58 2182
60 2234
59 2245
62 2387
61 2392
63 2460
64 2478
66 2613
65 2655
67 2740
68 2753
78 2881
77 2919
79 2921
76 2928
75 2954
80 2958
69 2969
70 3014
81 3014
71 3030
72 3056
82 3067
74 3073
73 3075
120 3157
83 3175
84 3381
85 3433
86 3627
87 3846
88 4098
89 4417
90 4535
119 4951
91 5096
92 5544
93 6045
94 6475
95 6913
118 7089
96 7211
97 7697
98 7877
99 8118
100 8194
101 8235
102 8280
103 8496
104 8740
105 9144
117 9335
106 9571
107 10767
116 11688
108 12174
109 13664
115 14461
110 15637
114 16983
111 17347
113 18332
112 18698