NGS_DNA
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Dependencies

1) Dependency tree

1
- BWA (0.7.15)
2
- sambamba (v0.6.6)
3
- GATK (3.7)
4
- io_lib (1.14.6)
5
- Python (2.7.10)
6
- Zlib (1.2.8)
7
- bzip2 (1.0.6)
8
- libreadline (6.3)
9
o ncursus (5.9)
10
- Picard (2.9.0)
11
o R(3.3.1)
12
• libreadline (6.3)
13
• ncursus (5.9)
14
• libjpeg-turbo (1.4.2)
15
• NASM(2.11.08)
16
• LibTIFF (4.0.4)
17
• Tk (8.6.4)
18
o Tcl (8.6.4.)
19
• Zlib (1.2.8)
20
• cUrl (7.47.1)
21
• libxml2 (2.9.2)
22
• cairo (1.14.6)
23
o bzip2 (1.0.6)
24
o pixman (0.32.8)
25
o fontconfig (2.11.94)
26
• freetype (2.6.1)
27
o libpng (1.6.21)
28
• zlib (1.2.8)
29
o expat (2.1.0)
30
• PCRE (8.38)
31
• Java (1.8.0_45)
32
o Java (1.7.0_80)
33
- HTSlib(1.3.2)
34
- cutadapt (1.9.1)
35
- ngs-utils (16.12.1)
36
o Text-CSV (1.33)
37
o Log-Log4Perl (1.46)
38
- Molgenis-Compute (16.08.1)
39
- CmdLineAnnotator (1.9.0)
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2) NGS_DNA-3.4.0 pipeline dependencies

1
('BWA', '0.7.15', '', ('foss', '2015b')),
2
('BEDTools', '2.25.0', '', ('foss', '2015b')),
3
('CoNVaDING', '1.1.6', '', ('dummy', '')),
4
('Molgenis-Compute', 'v17.08.1', '-Java-1.8.0_74'),
5
('FastQC', '0.11.5', '-Java-1.8.0_74'),
6
('GATK', '3.7', '-Java-1.8.0_74'),
7
('Gavin-ToolPack', '1.0', '-Java-1.8.0_74'),
8
('io_lib', '1.14.6', '', ('foss', '2015b')),
9
('manta','1.2.1', '', ('foss', '2015b')),
10
('snpEff', '4.3', '-Java-1.7.0_80'),
11
('ngs-utils', '17.11.1', '', ('dummy', '')),
12
('PerlPlus', '5.22.0', '-v17.08.1', ('foss', '2015b')),
13
('pigz', '2.3.1', '', ('foss', '2015b')),
14
('picard', '2.9.0', '-Java-1.8.0_74'),
15
('sambamba', 'v0.6.6', '', ('foss', '2015b')),
16
('seqtk', '1.2', '', ('foss', '2015b')),
17
('SAMtools', '1.2', '', ('foss', '2015b')),
18
('HTSlib', '1.3.2', '', ('foss', '2015b')),
19
('CmdLineAnnotator', '1.21.1', '-Java-1.8.0_45'),
20
('xhmm', '2016-01-04-cc14e528d909', '', ('foss', '2015b')),
21
('CADD', 'v1.3', '', ('dummy', '')),
22
('multiqc', '1.0','-Python-2.7.11', ('foss','2015b')),
23
('VEP', '90.5', '', ('dummy', '')),
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