-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathheader.html
More file actions
94 lines (94 loc) · 3.69 KB
/
Copy pathheader.html
File metadata and controls
94 lines (94 loc) · 3.69 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
<nav>
<ul class="menu">
<li><a href=""><span>Alignment</span></a>
<ul>
<li><a href="abra.html"><span>abra</span></a></li>
<li><a href="diamond.html"><span>diamond</span></a></li>
<li><a href="bowtie.html"><span>bowtie</span></a></li>
<li><a href="bwa.html"><span>bwa</span></a></li>
<li><a href="shrimp.html"><span>shrimp</span></a></li>
<li><a href="tophat.html"><span>tophat</span></a></li>
<li><a href="blast.html"><span>blast+</span></a></li>
<li><a href="mosaik.html"><span>mosaik</span></a></li>
<li><a href="mauve.html"><span>mauve</span></a></li>
<li><a href="mummer.html"><span>mummer</span></a></li>
<li><a href="star.html"><span>star</span></a></li>
<li><a href="bismark.html"><span>bismark</span></a></li>
</ul>
</li>
<li><a href=""><span>Conversion utilities</span></a>
<ul>
<li><a href="samtools.html"><span>samtools</span></a></li>
<li><a href="bedtools.html"><span>bedtools</span></a></li>
<li><a href="vcftools.html"><span>vcftools</span></a></li>
<li><a href="sra.html"><span>sra</span></a></li>
<li><a href="picard.html"><span>picard</span></a></li>
</ul>
</li>
<li><a href=""><span>Variant callers</span></a>
<ul>
<li><a href="gatk.html"><span>gatk</span></a></li>
<li><a href="mutect.html"><span>mutect</span></a></li>
<li><a href="varscan2.html"><span>varscan2</span></a></li>
<li><a href="lofreq.html"><span>lofreq</span></a></li>
</ul>
</li>
<li><a href=""><span>Annotation</span></a>
<ul>
<li><a href="annovar.html"><span>annovar</span></a></li>
<li><a href="snpeff.html"><span>snpeff</span></a></li>
<li><a href="ngsrich.html"><span>ngsrich</span></a></li>
</ul>
</li>
<li><a href=""><span>Assembling</span></a>
<ul>
<li><a href="spades.html"><span>spades</span></a></li>
<li><a href="velvet.html"><span>velvet</span></a></li>
<li><a href="ray.html"><span>ray</span></a></li>
<li><a href="cisa.html"><span>cisa</span></a></li>
<li><a href="pagit.html"><span>pagit</span></a></li>
</ul>
</li>
<li><a href=""><span>Peak finders</span></a>
<ul>
<li><a href="macs.html"><span>macs</span></a></li>
<li><a href="peakranger.html"><span>peakranger</span></a></li>
<li><a href="sicer.html"><span>sicer</span></a></li>
</ul>
</li>
<li><a href=""><span>RNA-Seq</span></a>
<ul>
<li><a href="cufflinks.html"><span>cufflinks</span></a></li>
<li><a href="htseq.html"><span>htseq</span></a></li>
<li><a href="splicetrap.html"><span>splicetrap</span></a></li>
<li><a href="chimerascan.html"><span>chimerascan</span></a></li>
<li><a href="reditools.html"><span>reditools</span></a></li>
</ul>
</li>
<li><a href=""><span>Quality control</span></a>
<ul>
<li><a href="fastqc.html"><span>fastqc</span></a></li>
<li><a href="ngsqctoolkit.html"><span>ngsqctoolkit</span></a></li>
<li><a href="trimmomatic.html"><span>trimmomatic</span></a></li>
</ul>
</li>
<li><a href=""><span>Metagenomics</span></a>
<ul>
<li><a href="concoct.html"><span>concoct</span></a></li>
<li><a href="qiime.html"><span>qiime</span></a></li>
</ul>
</li>
<li><a href=""><span>General purpose</span></a>
<ul>
<li><a href="bioconductor.html"><span>bioconductor</span></a></li>
<li><a href="biopython.html"><span>biopython</span></a></li>
<li><a href="cluto.html"><span>cluto</span></a></li>
<li><a href="igvtools.html"><span>igvtools</span></a></li>
<li><a href="idl.html"><span>idl</span></a></li>
<li><a href="mrjob.html"><span>mrjob</span></a></li>
<li><a href="r.html"><span>r</span></a></li>
<li><a href="emboss.html"><span>emboss</span></a></li>
</ul>
</li>
</ul>
</nav>