STOPGAP is a subtomogram averaging workflow written in MATLAB for performing a number of subtomogram averaging tasks including template matching, high-resolution alignment and averaging, and classification. Supplied is the source code, a set of example bash scripts, and instructions on how to compile and run STOPGAP. Pre-compiled binaries are also supplied; these were compiled using MATLAB R2020b. STOPGAP is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. STOPGAP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.