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
|
Source: plasmidid
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Steffen Moeller <moeller@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all,
help2man,
ncbi-blast+ <!nocheck>,
bedtools <!nocheck>,
bowtie2 <!nocheck>,
samtools <!nocheck>,
prokka <!nocheck>,
cd-hit <!nocheck>,
mash <!nocheck>,
circos <!nocheck>
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/plasmidid
Vcs-Git: https://salsa.debian.org/med-team/plasmidid.git
Homepage: https://github.com/BU-ISCIII/plasmidID
Rules-Requires-Root: no
Package: plasmidid
Architecture: any
Depends: ${misc:Depends},
${perl:Depends},
${python3:Depends},
ncbi-blast+,
bedtools,
bowtie2,
samtools,
prokka,
cd-hit,
mash,
circos
Recommends: trimmomatic,
spades,
python3-biopython,
python3-numpy,
python3-pandas
Description: mapping-based, assembly-assisted plasmid identification tool
PlasmidID is a mapping-based, assembly-assisted plasmid identification
tool that analyzes and gives graphic solution for plasmid
identification.
.
PlasmidID is a computational pipeline that maps Illumina reads over
plasmid database sequences. The k-mer filtered, most covered
sequences are clustered by identity to avoid redundancy and the
longest are used as scaffold for plasmid reconstruction. Reads are
assembled and annotated by automatic and specific annotation. All
information generated from mapping, assembly, annotation and local
alignment analyses is gathered and accurately represented in a
circular image which allow user to determine plasmidic composition in
any bacterial sample.
|
