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
|
Source: parsnp
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Étienne Mollier <emollier@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
python3-all-dev,
python3-setuptools,
cython3,
libmuscle-dev
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/parsnp
Vcs-Git: https://salsa.debian.org/med-team/parsnp.git
Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html
Rules-Requires-Root: no
Package: parsnp
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-biopython,
python3-numpy,
python3-pyspoa,
python3-tqdm,
fasttree,
harvest-tools,
mummer,
phipack,
python3,
raxml,
time
Recommends: python3-dendropy
Description: rapid core genome multi-alignment
Parsnp was designed to align the core genome of hundreds to thousands of
bacterial genomes within a few minutes to few hours. Input can be both
draft assemblies and finished genomes, and output includes variant (SNP)
calls, core genome phylogeny and multi-alignments. Parsnp leverages
contextual information provided by multi-alignments surrounding SNP
sites for filtration/cleaning, in addition to existing tools for
recombination detection/filtration and phylogenetic reconstruction.
|
