contig-puller

Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence

Author

Jason Kwong (@kwongjc)
GitHub: kwongj

Dependencies

• Python 3.x
• BioPython
• Prokka

Usage

$ contig-puller.py -h

usage: 
  contig-puller.py --db DBFILE --out OUTFILE --anno ANNOFILE [OPTIONS] FASTA-1 FASTA-2 ... FASTA-N

Extracts contigs containing a target sequence (eg. gene) from several multi-FASTA assemblies 
 and aligns the contigs at the target sequence

positional arguments:
  FASTA            FASTA assemblies to search

optional arguments:
  -h, --help       show this help message and exit
  --db DBFILE      target sequence (FASTA) to search for (REQUIRED to create
                   BLAST database)
  --id ID          percentage identity cutoff (default=100)
  --out OUTFILE    output file (default=contigs.gbk)
  --anno ANNOFILE  reference proteins.faa file to annotate from (optional |
                   requires Prokka to be installed)
  --cpus CPUS      number of cpus to use (default=8)
  --version        show program's version number and exit

Requires:

• Target sequence in FASTA format to search for eg. blaKPC-2
• Assemblies to search for target sequence

Options:

• Set BLAST search %identity cutoff (default = 100) using --id
• Specify proteins.faa file to annotate from using --anno
  (recommended to visualise surrounding context of target sequence)

Bugs

Please submit via the GitHub issues page: https://github.com/kwongj/contig-puller/issues

Software Licence

GPLv2: https://github.com/kwongj/contig-puller/blob/master/LICENSE

Other links

• Prokka