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
|
Source: roary
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
dh-dist-zilla,
libdist-zilla-plugin-podweaver-perl,
bioperl,
libarray-utils-perl,
libenv-path-perl,
libexception-class-perl,
libfile-find-rule-perl,
libfile-grep-perl,
libfile-slurper-perl,
libfile-which-perl,
libfindbin-libs-perl,
libgraph-perl,
libgraph-readwrite-perl,
liblog-log4perl-perl,
libmoose-perl,
libperlio-utf8-strict-perl,
libtest-most-perl,
libtest-file-perl,
libtest-files-perl,
libtest-output-perl,
libtext-csv-perl,
bedtools,
cd-hit,
ncbi-blast+,
mcl,
parallel,
prank,
r-base-core,
mafft,
fasttree
Build-Depends-Indep: perl
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/roary
Vcs-Git: https://salsa.debian.org/med-team/roary.git
Homepage: http://sanger-pathogens.github.io/Roary/
Package: roary
Architecture: all
Depends: ${perl:Depends},
${misc:Depends},
bioperl,
libarray-utils-perl,
libdigest-md5-file-perl,
libenv-path-perl,
libexception-class-perl,
libfile-find-rule-perl,
libfile-grep-perl,
libfile-slurper-perl,
libfile-which-perl,
libfindbin-libs-perl,
libgraph-perl,
libgraph-readwrite-perl,
liblog-log4perl-perl,
libmoose-perl,
libperlio-utf8-strict-perl,
libtest-most-perl,
libtest-file-perl,
libtest-files-perl,
libtest-output-perl,
libtext-csv-perl,
bedtools,
cd-hit,
ncbi-blast+,
mcl,
parallel,
prank,
r-base-core,
r-cran-ggplot2,
mafft,
fasttree
Description: high speed stand alone pan genome pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated
assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates
the pan genome. Using a standard desktop PC, it can analyse datasets with
thousands of samples, something which is computationally infeasible with
existing methods, without compromising the quality of the results. 128 samples
can be analysed in under 1 hour using 1 GB of RAM and a single processor.
To perform this analysis using existing methods would take weeks and hundreds
of GB of RAM. Roary is not intended for meta-genomics or for comparing
extremely diverse sets of genomes.
|
