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
|
Source: spades
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Sascha Steinbiss <satta@debian.org>,
Michael R. Crusoe <crusoe@debian.org>,
Alexandre Mestiashvili <mestia@debian.org>,
Étienne Mollier <emollier@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
clang-format,
clang-tidy,
clang-tools,
cmake,
python3-all,
zlib1g-dev,
libbz2-dev,
libbam-dev,
libbamtools-dev,
libc++-dev,
libhts-dev,
libnlopt-dev,
libnlopt-cxx-dev,
libssw-dev,
libzstd-dev,
llvm-dev,
python3-yaml,
python3-joblib,
asciidoctor,
bwa,
libbwa-dev,
lynx
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/spades
Vcs-Git: https://salsa.debian.org/med-team/spades.git
Homepage: https://github.com/ablab/spades
Rules-Requires-Root: no
Package: spades
Architecture: amd64
Depends: ${shlibs:Depends},
${python3:Depends},
${misc:Depends},
python3,
python3-joblib,
python3-packaging,
python3-yaml,
bwa,
bamtools,
samtools
Description: genome assembler for single-cell and isolates data sets
The SPAdes – St. Petersburg genome assembler is intended for both
standard isolates and single-cell MDA bacteria assemblies. It works
with Illumina or IonTorrent reads and is capable of providing hybrid
assemblies using PacBio and Sanger reads. You can also provide
additional contigs that will be used as long reads.
.
This package provides the following additional pipelines:
* metaSPAdes – a pipeline for metagenomic data sets
* plasmidSPAdes – a pipeline for extracting and assembling plasmids
from WGS data sets
* metaplasmidSPAdes – a pipeline for extracting and assembling
plasmids from metagenomic data sets
* rnaSPAdes – a de novo transcriptome assembler from RNA-Seq data
* truSPAdes – a module for TruSeq barcode assembly
* biosyntheticSPAdes – a module for biosynthetic gene cluster
assembly with paired-end reads
.
SPAdes provides several stand-alone binaries with relatively simple
command-line interface: k-mer counting (spades-kmercounter), assembly
graph construction (spades-gbuilder) and long read to graph aligner
(spades-gmapper).
|
