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Widely-used Radseq analysis software protocol by Julian Catchen.



There are 5 stages:

  • Reads are demultiplexed and cleaned by process_radtags.
  • Loci must be built with ustacks (if de-nov/no-reference) or pstacks (if with reference)
  • Creating the catalog of loci cstacks
  • Matching against catalog with sstacks.
  • Either the populations or genotypes program is executed, depending on input datasets,

setting up database on mysql

  • Create database, you must have the appropriate privileges for this. If you do, the command will be something like:
echo "CREATE DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p
  • Ensure $STACKSROOTDIR/share/stacks/sql/my.cnf is set up properly
  • Ensure modification privileges for the user
  • Load stack.sql schema onto the database. It's in $STACKSROOTDIR/share/stacks/sql/stacks.sql, i.e.
mysql <mydbname> -h <name_of_server_running_mysql> -u <myusername> -p < $STACKSROOTDIR/share/stacks/sql/stacks.sql
  • For whatever reason one can also start over by deleting a database. Care should be taken with a step like this, just in case one deletes the wrong database. The delete command's keyword is in fact "DROP" and woudl be run like this:
echo "DROP DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p