- recipe pgcgap
A prokaryotic genomics and comparative genomics analysis pipeline
- Homepage
https://github.com/liaochenlanruo/pgcgap/blob/master/README.md
- Documentation
- Developer docs
- License
GPL / GPLv3
- Recipe
- Links
biotools: pgcgap
PGCGAP is a pipeline for prokaryotic comparative genomics analysis. It can take the pair-end reads, ONT reads or PacBio reads as input. In addition to genome assembly, gene prediction and annotation, it can also get common comparative genomics analysis results such as phylogenetic trees of single-core proteins and core SNPs, pan-genome, whole-genome Average Nucleotide Identity (ANI), orthogroups and orthologs, COG annotations, substitutions (SNPs) and insertions/deletions (indels), and antimicrobial and virulence genes mining with only one line of commands.
- package pgcgap¶
-
- Versions
1.0.35-0
,1.0.34-0
,1.0.33-0
,1.0.32-0
,1.0.31-0
,1.0.30-0
,1.0.29-0
,1.0.28-0
,1.0.27-0
,1.0.35-0
,1.0.34-0
,1.0.33-0
,1.0.32-0
,1.0.31-0
,1.0.30-0
,1.0.29-0
,1.0.28-0
,1.0.27-0
,1.0.26-0
,1.0.25-0
,1.0.24-0
,1.0.23-0
,1.0.22-0
,1.0.21-0
,1.0.20-0
,1.0.19-2
,1.0.19-1
,1.0.19-0
,1.0.18-1
,1.0.18-0
,1.0.17-0
,1.0.16-0
,1.0.15-0
,1.0.14-0
,1.0.13-1
,1.0.13-0
,1.0.12-1
,1.0.12-0
,1.0.11-1
,1.0.11-0
,1.0.10-2
,1.0.10-1
,1.0.10-0
,1.0.9-2
,1.0.9-1
,1.0.9-0
,1.0.8-0
,1.0.7-0
,1.0.6-0
,1.0.5-0
,1.0.4-0
,1.0.3-0
,1.0.2-4
,1.0.2-3
,1.0.2-2
,1.0.2-1
,1.0.1-1
,1.0.1-0
,1.0.0-0
- Depends
abricate
1.0.1.*
abyss
2.3.4.*
canu
2.1.1.*
coreutils
9.0.*
fastani
1.33.*
fastp
0.23.2.*
htslib
1.15.1.*
mamba
0.22.1.*
mash
2.3.*
matplotlib-base
3.5.1.*
muscle
5.1.*
numpy
1.21.5.*
orthofinder
2.5.4.*
pal2nal
14.1.*
panaroo
1.2.10.*
pandas
1.3.5.*
perl
>=5.32.1,<6.0a0 *_perl5
prokka
>=1.14.5
r-base
>=4.1.1
seaborn
0.11.2.*
sickle-trim
1.33.*
snippy
4.6.0.*
snpeff
5.0.*
trimal
1.4.1.*
unicycler
0.5.0.*
wget
1.20.3.*
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install pgcgap
and update with:
conda update pgcgap
or use the docker container:
docker pull quay.io/biocontainers/pgcgap:<tag>
(see pgcgap/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pgcgap/README.html)