gapseq

Informed prediction and analysis of bacteria metabolic pathways and genome-scale networks

gapseq is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. Based on genomic information and databases for pathways and reactions, gapseq can be used for:

prediction of metabolic pathways from various databases
transporter inference
metabolic model creation
multi-step gap filling

Installation

Ubuntu/Debian/Mint

sudo apt install ncbi-blast+ git libglpk-dev r-base-core exonerate bedtools barrnap
R -e 'install.packages(c("data.table", "stringr", "sybil", "getopt", "reshape2", "doParallel", "foreach", "R.utils", "stringi"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
git clone https://github.com/jotech/gapseq && cd gapseq

Centos/Fedora/RHEL

sudo yum install ncbi-blast+ git glpk-devel BEDTools exonerate hmmer
git clone https://github.com/tseemann/barrnap.git
export PATH=$PATH:barrnap/bin/barrnap # needs to be permanent => .bashrc ?
R -e 'install.packages(c("data.table", "stringr", "sybil", "getopt", "reshape2", "doParallel", "foreach", "R.utils", "stringi"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
git clone https://github.com/jotech/gapseq && cd gapseq

MacOS

using homebrew

brew install git glpk blast bedtools r brewsci/bio/barrnap
R -e 'install.packages(c("data.table", "stringr", "sybil", "getopt", "reshape2", "doParallel", "foreach", "R.utils", "stringi"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
git clone https://github.com/jotech/gapseq && cd gapseq

Troubleshooting

at least ncbi blast version 2.2.27 (4/2013) is needed. If your disribution only contains an older version, try to download a binary directly from ncbi
If you are getting the installation error 'lib = "../R/library"' is not writable while installing the R packages, then try this command beforehand:

Rscript -e 'if( file.access(Sys.getenv("R_LIBS_USER"), mode=2) == -1 ) dir.create(path = Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE)'

Quickstart

This predicts network candidate reactions, builds a draft model and performs gap filling:

./gapseq doall toy/myb71.fna

Do the same but with a defined medium for gap filling:

./gapseq doall toy/ecoli.fna.gz dat/media/MM_glu.csv

Pathway analysis

Search for chitin pathways:

./gapseq find -p chitin toy/myb71.fna.gz

Check for a certain enzyme availability, for example cytochrome c oxidases (oxidase test)

./gapseq find -e 1.9.3.1 toy/ecoli.fna.gz

Search for enzymes by name:

./gapseq find -r ligninase toy/myb71.fna.gz

Creation and gap filling of metabolic models

Metabolic pathway analysis

./gapseq find -p all toy/myb71.fna
./gapseq find-transport toy/myb71.fna

Creation of draft model

 ./gapseq draft -r toy/myb71-all-Reactions.tbl -t toy/myb71-Transporter.tbl -p toy/myb71-all-Pathways.tbl -c toy/myb71.fna.gz

Gap filling

gapseq fill -m toy/myb71-draft.RDS -c toy/myb71-rxnWeights.RDS -n dat/media/TSBmed.csv

PoeticPremium6/gapseq