Stacks

Widely-used Radseq analysis software protocol by Julian Catchen.

Stages

Overall

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

Installation and compilation (admins only)

Stacks uses the usual configure && make && make install routine, but has several configure options. Primarily there is bam: this is not precisely bamtools, but rather samtools, though the directories say bam and not samtools ... the documentation isn't very clear. In any case, this is a model of a workable compile line.

./configure --enable-bam --with-bam-include-path=/usr/local/include/bam --with-bam-lib-path=/usr/local/lib