The shell script contains various functions for managing and constructing local sequence database.
seqdb [subcommand] [options]
Available subcommands:
build_db construct a local sequence database
extract retrieve a target sequence from database
remove remove an existing target from database
insert add a new sequence to database
replace replace sequence of an existing target with a new sequence
unbuild_db deconstruct a local sequence database
search identify significant hits from an existing database given a query sequence
build_tree construct a cgSNP tree from closest genomic neighbours in the database
- Clone the repository
git clone https://github.com/jimmyliu1326/seqdb.git
- Modify file permissions
chmod +x seqdb/seqdb
- Add seqdb to PATH by including the following line in ~/.bashrc
export PATH="/path/to/seqdb:$PATH"
The following dependencies must be installed and added to PATH:
- seqkit >= 0.13.0
- mash >= 2.2.2
- phame = 1.0.3
- mashtree >= 1.1.2
- picard >= 2.23.3
- kipper >= 1.0.0