gapseq

The gapseq paper is publised in Genome Biology 2021 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02295-1).

All required tools has been installed on the lab server  /home/pubadmin/programs/gapseq.

To run gapseq properly, it has to be installed in the user's local folder as follows:

## Install gapseq locally

git clone https://github.com/jotech/gapseq && cd gapseq

## Download Bacteria and Archaea databases

src/update_sequences.sh
src/update_sequences.sh Archaea
  
## Test the gapseq installation

  ./gapseq test

## Download genome assemblies from NCBI

  wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Lactobacillus_johnsonii/representative/GCF_014841035.1_ASM1484103v1/GCF_014841035.1_ASM1484103v1_genomic.fna.gz -P /home/xuejian/Evonik/Data/
  mv /home/xuejian/Evonik/Data/GCF_014841035.1_ASM1484103v1_genomic.fna.gz /home/xuejian/Evonik/Data/Lactobacillus_johnsonii.fna.gz



Here is an example to run the gapseq pipeline:

  #!/bin/bash
  # set the path to gapseq
  gapseqdir=/home/username/gapseq
  workdir=/home/username/test

  data=$workdir/Data
  outdir=$workdir/Results

  gapseq=$gapseqdir/./gapseq
  taxonomy=Bacteria

  modelA="Lactobacillus_johnsonii"

  cd $outdir

  # Reaction & Pathway prediction
  $gapseq find -p all -v 0 -b 200 -t $taxonomy -m $taxonomy $data/$modelA.fna.gz

  # Transporter prediction
  $gapseq find-transport -b 200 $data/$modelA.fna.gz 

  # Building Draft Model - based on Reaction-, Pathway-, and Transporter prediction
  $gapseq draft -r $outdir/$modelA-all-Reactions.tbl -t $outdir/$modelA-Transporter.tbl -p $outdir/$modelA-all-Pathways.tbl -c $data/$modelA.fna.gz -u 200 -l 100  -b $taxonomy

  # get growth medium
  Rscript $gapseqdir/src/predict_medium.R -m $outdir/$modelA-draft.RDS -p $outdir/$modelA-all-Pathways.tbl

  # Gapfilling
  $gapseq fill -m $outdir/$modelA-draft.RDS -n $outdir/$modelA-medium.csv -c $outdir/$modelA-rxnWeights.RDS -g $outdir/$modelA-rxnXgenes.RDS -b 100