recipe pgcgap

A prokaryotic genomics and comparative genomics analysis pipeline

Homepage

https://github.com/liaochenlanruo/pgcgap/blob/master/README.md

Documentation

https://liaochenlanruo.fun/pgcgap/

Developer docs

https://github.com/liaochenlanruo/pgcgap/tree/master

License

GPL / GPLv3

Recipe

/pgcgap/meta.yaml

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.*

• openjdk

• orthofinder 2.5.4.*

• pal2nal 14.1.*

• panaroo 1.2.10.*

• pandas 1.3.5.*

• perl >=5.32.1,<6.0a0 *_perl5

• perl-data-dumper

• perl-file-copy-recursive

• perl-file-tee

• perl-parallel-forkmanager

• perl-pod-usage

• perl-posix

• prokka >=1.14.5

• r-base >=4.1.1

• r-corrplot

• r-ggplot2

• r-gplots

• r-pheatmap

• r-plotrix

• 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

• bttoxin_scanner

• bttcmp

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

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